Matching Items (47)
Description
Surgery as a profession requires significant training to improve both clinical decision making and psychomotor proficiency. In the medical knowledge domain, tools have been developed, validated, and accepted for evaluation of surgeons' competencies. However, assessment of the psychomotor skills still relies on the Halstedian model of apprenticeship, wherein surgeons are observed during residency for judgment of their skills. Although the value of this method of skills assessment cannot be ignored, novel methodologies of objective skills assessment need to be designed, developed, and evaluated that augment the traditional approach. Several sensor-based systems have been developed to measure a user's skill quantitatively, but use of sensors could interfere with skill execution and thus limit the potential for evaluating real-life surgery. However, having a method to judge skills automatically in real-life conditions should be the ultimate goal, since only with such features that a system would be widely adopted. This research proposes a novel video-based approach for observing surgeons' hand and surgical tool movements in minimally invasive surgical training exercises as well as during laparoscopic surgery. Because our system does not require surgeons to wear special sensors, it has the distinct advantage over alternatives of offering skills assessment in both learning and real-life environments. The system automatically detects major skill-measuring features from surgical task videos using a computing system composed of a series of computer vision algorithms and provides on-screen real-time performance feedback for more efficient skill learning. Finally, the machine-learning approach is used to develop an observer-independent composite scoring model through objective and quantitative measurement of surgical skills. To increase effectiveness and usability of the developed system, it is integrated with a cloud-based tool, which automatically assesses surgical videos upload to the cloud.
ContributorsIslam, Gazi (Author) / Li, Baoxin (Thesis advisor) / Liang, Jianming (Thesis advisor) / Dinu, Valentin (Committee member) / Greenes, Robert (Committee member) / Smith, Marshall (Committee member) / Kahol, Kanav (Committee member) / Patel, Vimla L. (Committee member) / Arizona State University (Publisher)
Created2013
Description
The apolipoprotein E (APOE) e4 genotype is the most prevalent known genetic risk factor for Alzheimer's disease (AD). In this paper, we examined the longitudinal effect of APOE e4 on hippocampal morphometry in Alzheimer's Disease Neuroimaging Initiative (ADNI). Generally, atrophy of hippocampus has more chance occurs in AD patients who carrying the APOE e4 allele than those who are APOE e4 noncarriers. Also, brain structure and function depend on APOE genotype not just for Alzheimer's disease patients but also in health elderly individuals, so APOE genotyping is considered critical in clinical trials of Alzheimer's disease. We used a large sample of elderly participants, with the help of a new automated surface registration system based on surface conformal parameterization with holomorphic 1-forms and surface fluid registration. In this system, we automatically segmented and constructed hippocampal surfaces from MR images at many different time points, such as 6 months, 1- and 2-year follow up. Between the two different hippocampal surfaces, we did the high-order correspondences, using a novel inverse consistent surface fluid registration method. At each time point, using Hotelling's T^2 test, we found significant morphological deformation in APOE e4 carriers relative to noncarriers in the entire cohort as well as in the non-demented (pooled MCI and control) subjects, affecting the left hippocampus more than the right, and this effect was more pronounced in e4 homozygotes than heterozygotes.
ContributorsLi, Bolun (Author) / Wang, Yalin (Thesis advisor) / Maciejewski, Ross (Committee member) / Liang, Jianming (Committee member) / Arizona State University (Publisher)
Created2015
Description
Advances in data collection technologies have made it cost-effective to obtain heterogeneous data from multiple data sources. Very often, the data are of very high dimension and feature selection is preferred in order to reduce noise, save computational cost and learn interpretable models. Due to the multi-modality nature of heterogeneous data, it is interesting to design efficient machine learning models that are capable of performing variable selection and feature group (data source) selection simultaneously (a.k.a bi-level selection). In this thesis, I carry out research along this direction with a particular focus on designing efficient optimization algorithms. I start with a unified bi-level learning model that contains several existing feature selection models as special cases. Then the proposed model is further extended to tackle the block-wise missing data, one of the major challenges in the diagnosis of Alzheimer's Disease (AD). Moreover, I propose a novel interpretable sparse group feature selection model that greatly facilitates the procedure of parameter tuning and model selection. Last but not least, I show that by solving the sparse group hard thresholding problem directly, the sparse group feature selection model can be further improved in terms of both algorithmic complexity and efficiency. Promising results are demonstrated in the extensive evaluation on multiple real-world data sets.
ContributorsXiang, Shuo (Author) / Ye, Jieping (Thesis advisor) / Mittelmann, Hans D (Committee member) / Davulcu, Hasan (Committee member) / He, Jingrui (Committee member) / Arizona State University (Publisher)
Created2014
Description
Detecting anatomical structures, such as the carina, the pulmonary trunk and the aortic arch, is an important step in designing a CAD system of detection Pulmonary Embolism. The presented CAD system gets rid of the high-level prior defined knowledge to become a system which can easily extend to detect other anatomic structures. The system is based on a machine learning algorithm --- AdaBoost and a general feature --- Haar. This study emphasizes on off-line and on-line AdaBoost learning. And in on-line AdaBoost, the thesis further deals with extremely imbalanced condition. The thesis first reviews several knowledge-based detection methods, which are relied on human being's understanding of the relationship between anatomic structures. Then the thesis introduces a classic off-line AdaBoost learning. The thesis applies different cascading scheme, namely multi-exit cascading scheme. The comparison between the two methods will be provided and discussed. Both of the off-line AdaBoost methods have problems in memory usage and time consuming. Off-line AdaBoost methods need to store all the training samples and the dataset need to be set before training. The dataset cannot be enlarged dynamically. Different training dataset requires retraining the whole process. The retraining is very time consuming and even not realistic. To deal with the shortcomings of off-line learning, the study exploited on-line AdaBoost learning approach. The thesis proposed a novel pool based on-line method with Kalman filters and histogram to better represent the distribution of the samples' weight. Analysis of the performance, the stability and the computational complexity will be provided in the thesis. Furthermore, the original on-line AdaBoost performs badly in imbalanced conditions, which occur frequently in medical image processing. In image dataset, positive samples are limited and negative samples are countless. A novel Self-Adaptive Asymmetric On-line Boosting method is presented. The method utilized a new asymmetric loss criterion with self-adaptability according to the ratio of exposed positive and negative samples and it has an advanced rule to update sample's importance weight taking account of both classification result and sample's label. Compared to traditional on-line AdaBoost Learning method, the new method can achieve far more accuracy in imbalanced conditions.
ContributorsWu, Hong (Author) / Liang, Jianming (Thesis advisor) / Farin, Gerald (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis studies recommendation systems and considers joint sampling and learning. Sampling in recommendation systems is to obtain users' ratings on specific items chosen by the recommendation platform, and learning is to infer the unknown ratings of users to items given the existing data. In this thesis, the problem is formulated as an adaptive matrix completion problem in which sampling is to reveal the unknown entries of a $U\times M$ matrix where $U$ is the number of users, $M$ is the number of items, and each entry of the $U\times M$ matrix represents the rating of a user to an item. In the literature, this matrix completion problem has been studied under a static setting, i.e., recovering the matrix based on a set of partial ratings. This thesis considers both sampling and learning, and proposes an adaptive algorithm. The algorithm adapts its sampling and learning based on the existing data. The idea is to sample items that reveal more information based on the previous sampling results and then learn based on clustering. Performance of the proposed algorithm has been evaluated using simulations.
ContributorsZhu, Lingfang (Author) / Xue, Guoliang (Thesis advisor) / He, Jingrui (Committee member) / Tong, Hanghang (Committee member) / Arizona State University (Publisher)
Created2015
Description
Diffusion processes in networks can be used to model many real-world processes, such as the propagation of a rumor on social networks and cascading failures on power networks. Analysis of diffusion processes in networks can help us answer important questions such as the role and the importance of each node in the network for spreading the diffusion and how to top or contain a cascading failure in the network. This dissertation consists of three parts.
In the first part, we study the problem of locating multiple diffusion sources in networks under the Susceptible-Infected-Recovered (SIR) model. Given a complete snapshot of the network, we developed a sample-path-based algorithm, named clustering and localization, and proved that for regular trees, the estimators produced by the proposed algorithm are within a constant distance from the real sources with a high probability. Then, we considered the case in which only a partial snapshot is observed and proposed a new algorithm, named Optimal-Jordan-Cover (OJC). The algorithm first extracts a subgraph using a candidate selection algorithm that selects source candidates based on the number of observed infected nodes in their neighborhoods. Then, in the extracted subgraph, OJC finds a set of nodes that "cover" all observed infected nodes with the minimum radius. The set of nodes is called the Jordan cover, and is regarded as the set of diffusion sources. We proved that OJC can locate all sources with probability one asymptotically with partial observations in the Erdos-Renyi (ER) random graph. Multiple experiments on different networks were done, which show our algorithms outperform others.
In the second part, we tackle the problem of reconstructing the diffusion history from partial observations. We formulated the diffusion history reconstruction problem as a maximum a posteriori (MAP) problem and proved the problem is NP hard. Then we proposed a step-by- step reconstruction algorithm, which can always produce a diffusion history that is consistent with the partial observations. Our experimental results based on synthetic and real networks show that the algorithm significantly outperforms some existing methods.
In the third part, we consider the problem of improving the robustness of an interdependent network by rewiring a small number of links during a cascading attack. We formulated the problem as a Markov decision process (MDP) problem. While the problem is NP-hard, we developed an effective and efficient algorithm, RealWire, to robustify the network and to mitigate the damage during the attack. Extensive experimental results show that our algorithm outperforms other algorithms on most of the robustness metrics.
In the first part, we study the problem of locating multiple diffusion sources in networks under the Susceptible-Infected-Recovered (SIR) model. Given a complete snapshot of the network, we developed a sample-path-based algorithm, named clustering and localization, and proved that for regular trees, the estimators produced by the proposed algorithm are within a constant distance from the real sources with a high probability. Then, we considered the case in which only a partial snapshot is observed and proposed a new algorithm, named Optimal-Jordan-Cover (OJC). The algorithm first extracts a subgraph using a candidate selection algorithm that selects source candidates based on the number of observed infected nodes in their neighborhoods. Then, in the extracted subgraph, OJC finds a set of nodes that "cover" all observed infected nodes with the minimum radius. The set of nodes is called the Jordan cover, and is regarded as the set of diffusion sources. We proved that OJC can locate all sources with probability one asymptotically with partial observations in the Erdos-Renyi (ER) random graph. Multiple experiments on different networks were done, which show our algorithms outperform others.
In the second part, we tackle the problem of reconstructing the diffusion history from partial observations. We formulated the diffusion history reconstruction problem as a maximum a posteriori (MAP) problem and proved the problem is NP hard. Then we proposed a step-by- step reconstruction algorithm, which can always produce a diffusion history that is consistent with the partial observations. Our experimental results based on synthetic and real networks show that the algorithm significantly outperforms some existing methods.
In the third part, we consider the problem of improving the robustness of an interdependent network by rewiring a small number of links during a cascading attack. We formulated the problem as a Markov decision process (MDP) problem. While the problem is NP-hard, we developed an effective and efficient algorithm, RealWire, to robustify the network and to mitigate the damage during the attack. Extensive experimental results show that our algorithm outperforms other algorithms on most of the robustness metrics.
ContributorsChen, Zhen (Author) / Ying, Lei (Thesis advisor) / Tong, Hanghang (Thesis advisor) / Zhang, Junshan (Committee member) / He, Jingrui (Committee member) / Arizona State University (Publisher)
Created2018
Description
Network mining has been attracting a lot of research attention because of the prevalence of networks. As the world is becoming increasingly connected and correlated, networks arising from inter-dependent application domains are often collected from different sources, forming the so-called multi-sourced networks. Examples of such multi-sourced networks include critical infrastructure networks, multi-platform social networks, cross-domain collaboration networks, and many more. Compared with single-sourced network, multi-sourced networks bear more complex structures and therefore could potentially contain more valuable information.
This thesis proposes a multi-layered HITS (Hyperlink-Induced Topic Search) algorithm to perform the ranking task on multi-sourced networks. Specifically, each node in the network receives an authority score and a hub score for evaluating the value of the node itself and the value of its outgoing links respectively. Based on a recent multi-layered network model, which allows more flexible dependency structure across different sources (i.e., layers), the proposed algorithm leverages both within-layer smoothness and cross-layer consistency. This essentially allows nodes from different layers to be ranked accordingly. The multi-layered HITS is formulated as a regularized optimization problem with non-negative constraint and solved by an iterative update process. Extensive experimental evaluations demonstrate the effectiveness and explainability of the proposed algorithm.
This thesis proposes a multi-layered HITS (Hyperlink-Induced Topic Search) algorithm to perform the ranking task on multi-sourced networks. Specifically, each node in the network receives an authority score and a hub score for evaluating the value of the node itself and the value of its outgoing links respectively. Based on a recent multi-layered network model, which allows more flexible dependency structure across different sources (i.e., layers), the proposed algorithm leverages both within-layer smoothness and cross-layer consistency. This essentially allows nodes from different layers to be ranked accordingly. The multi-layered HITS is formulated as a regularized optimization problem with non-negative constraint and solved by an iterative update process. Extensive experimental evaluations demonstrate the effectiveness and explainability of the proposed algorithm.
ContributorsYu, Haichao (Author) / Tong, Hanghang (Thesis advisor) / He, Jingrui (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2018
Description
Unsupervised learning of time series data, also known as temporal clustering, is a challenging problem in machine learning. This thesis presents a novel algorithm, Deep Temporal Clustering (DTC), to naturally integrate dimensionality reduction and temporal clustering into a single end-to-end learning framework, fully unsupervised. The algorithm utilizes an autoencoder for temporal dimensionality reduction and a novel temporal clustering layer for cluster assignment. Then it jointly optimizes the clustering objective and the dimensionality reduction objective. Based on requirement and application, the temporal clustering layer can be customized with any temporal similarity metric. Several similarity metrics and state-of-the-art algorithms are considered and compared. To gain insight into temporal features that the network has learned for its clustering, a visualization method is applied that generates a region of interest heatmap for the time series. The viability of the algorithm is demonstrated using time series data from diverse domains, ranging from earthquakes to spacecraft sensor data. In each case, the proposed algorithm outperforms traditional methods. The superior performance is attributed to the fully integrated temporal dimensionality reduction and clustering criterion.
ContributorsMadiraju, NaveenSai (Author) / Liang, Jianming (Thesis advisor) / Wang, Yalin (Thesis advisor) / He, Jingrui (Committee member) / Arizona State University (Publisher)
Created2018
Description
This thesis presents a family of adaptive curvature methods for gradient-based stochastic optimization. In particular, a general algorithmic framework is introduced along with a practical implementation that yields an efficient, adaptive curvature gradient descent algorithm. To this end, a theoretical and practical link between curvature matrix estimation and shrinkage methods for covariance matrices is established. The use of shrinkage improves estimation accuracy of the curvature matrix when data samples are scarce. This thesis also introduce several insights that result in data- and computation-efficient update equations. Empirical results suggest that the proposed method compares favorably with existing second-order techniques based on the Fisher or Gauss-Newton and with adaptive stochastic gradient descent methods on both supervised and reinforcement learning tasks.
ContributorsBarron, Trevor (Author) / Ben Amor, Heni (Thesis advisor) / He, Jingrui (Committee member) / Levihn, Martin (Committee member) / Arizona State University (Publisher)
Created2019
Model Based Automatic and Robust Spike Sorting for Large Volumes of Multi-channel Extracellular Data
Description
Spike sorting is a critical step for single-unit-based analysis of neural activities extracellularly and simultaneously recorded using multi-channel electrodes. When dealing with recordings from very large numbers of neurons, existing methods, which are mostly semiautomatic in nature, become inadequate.
This dissertation aims at automating the spike sorting process. A high performance, automatic and computationally efficient spike detection and clustering system, namely, the M-Sorter2 is presented. The M-Sorter2 employs the modified multiscale correlation of wavelet coefficients (MCWC) for neural spike detection. At the center of the proposed M-Sorter2 are two automatic spike clustering methods. They share a common hierarchical agglomerative modeling (HAM) model search procedure to strategically form a sequence of mixture models, and a new model selection criterion called difference of model evidence (DoME) to automatically determine the number of clusters. The M-Sorter2 employs two methods differing by how they perform clustering to infer model parameters: one uses robust variational Bayes (RVB) and the other uses robust Expectation-Maximization (REM) for Student’s 𝑡-mixture modeling. The M-Sorter2 is thus a significantly improved approach to sorting as an automatic procedure.
M-Sorter2 was evaluated and benchmarked with popular algorithms using simulated, artificial and real data with truth that are openly available to researchers. Simulated datasets with known statistical distributions were first used to illustrate how the clustering algorithms, namely REMHAM and RVBHAM, provide robust clustering results under commonly experienced performance degrading conditions, such as random initialization of parameters, high dimensionality of data, low signal-to-noise ratio (SNR), ambiguous clusters, and asymmetry in cluster sizes. For the artificial dataset from single-channel recordings, the proposed sorter outperformed Wave_Clus, Plexon’s Offline Sorter and Klusta in most of the comparison cases. For the real dataset from multi-channel electrodes, tetrodes and polytrodes, the proposed sorter outperformed all comparison algorithms in terms of false positive and false negative rates. The software package presented in this dissertation is available for open access.
This dissertation aims at automating the spike sorting process. A high performance, automatic and computationally efficient spike detection and clustering system, namely, the M-Sorter2 is presented. The M-Sorter2 employs the modified multiscale correlation of wavelet coefficients (MCWC) for neural spike detection. At the center of the proposed M-Sorter2 are two automatic spike clustering methods. They share a common hierarchical agglomerative modeling (HAM) model search procedure to strategically form a sequence of mixture models, and a new model selection criterion called difference of model evidence (DoME) to automatically determine the number of clusters. The M-Sorter2 employs two methods differing by how they perform clustering to infer model parameters: one uses robust variational Bayes (RVB) and the other uses robust Expectation-Maximization (REM) for Student’s 𝑡-mixture modeling. The M-Sorter2 is thus a significantly improved approach to sorting as an automatic procedure.
M-Sorter2 was evaluated and benchmarked with popular algorithms using simulated, artificial and real data with truth that are openly available to researchers. Simulated datasets with known statistical distributions were first used to illustrate how the clustering algorithms, namely REMHAM and RVBHAM, provide robust clustering results under commonly experienced performance degrading conditions, such as random initialization of parameters, high dimensionality of data, low signal-to-noise ratio (SNR), ambiguous clusters, and asymmetry in cluster sizes. For the artificial dataset from single-channel recordings, the proposed sorter outperformed Wave_Clus, Plexon’s Offline Sorter and Klusta in most of the comparison cases. For the real dataset from multi-channel electrodes, tetrodes and polytrodes, the proposed sorter outperformed all comparison algorithms in terms of false positive and false negative rates. The software package presented in this dissertation is available for open access.
ContributorsMa, Weichao (Author) / Si, Jennie (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / He, Jingrui (Committee member) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2019