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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
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
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
The ability to profile proteins allows us to gain a deeper understanding of organization, regulation, and function of different biological systems. Many technologies are currently being used in order to accurately perform the protein profiling. Some of these technologies include mass spectrometry, microarray based analysis, and fluorescence microscopy. Deeper analysis of these technologies have demonstrated limitations which have taken away from either the efficiency or the accuracy of the results. The objective of this project was to develop a technology in which highly multiplexed single cell in situ protein analysis can be completed in a comprehensive manner without the loss of the protein targets. This was accomplished in the span of 3 steps which is referred to as the immunofluorescence cycle. Antibodies with attached fluorophores with the help of novel azide-based cleavable linker are used to detect protein targets. Fluorescence imaging and data storage procedures are done on the targets and then the fluorophores are cleaved from the antibodies without the loss of the protein targets. Continuous cycles of the immunofluorescence procedure can help create a comprehensive and quantitative profile of the protein. The development of such a technique will not only help us understand biological systems such as solid tumor, brain tissues, and developing embryos. But it will also play a role in real-world applications such as signaling network analysis, molecular diagnosis and cellular targeted therapies.
ContributorsGupta, Aakriti (Author) / Guo, Jia (Thesis director) / Liang, Jianming (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Computational visual aesthetics has recently become an active research area. Existing state-of-art methods formulate this as a binary classification task where a given image is predicted to be beautiful or not. In many applications such as image retrieval and enhancement, it is more important to rank images based on their aesthetic quality instead of binary-categorizing them. Furthermore, in such applications, it may be possible that all images belong to the same category. Hence determining the aesthetic ranking of the images is more appropriate. To this end, a novel problem of ranking images with respect to their aesthetic quality is formulated in this work. A new data-set of image pairs with relative labels is constructed by carefully selecting images from the popular AVA data-set. Unlike in aesthetics classification, there is no single threshold which would determine the ranking order of the images across the entire data-set.
This problem is attempted using a deep neural network based approach that is trained on image pairs by incorporating principles from relative learning. Results show that such relative training procedure allows the network to rank the images with a higher accuracy than a state-of-art network trained on the same set of images using binary labels. Further analyzing the results show that training a model using the image pairs learnt better aesthetic features than training on same number of individual binary labelled images.
Additionally, an attempt is made at enhancing the performance of the system by incorporating saliency related information. Given an image, humans might fixate their vision on particular parts of the image, which they might be subconsciously intrigued to. I therefore tried to utilize the saliency information both stand-alone as well as in combination with the global and local aesthetic features by performing two separate sets of experiments. In both the cases, a standard saliency model is chosen and the generated saliency maps are convoluted with the images prior to passing them to the network, thus giving higher importance to the salient regions as compared to the remaining. Thus generated saliency-images are either used independently or along with the global and the local features to train the network. Empirical results show that the saliency related aesthetic features might already be learnt by the network as a sub-set of the global features from automatic feature extraction, thus proving the redundancy of the additional saliency module.
This problem is attempted using a deep neural network based approach that is trained on image pairs by incorporating principles from relative learning. Results show that such relative training procedure allows the network to rank the images with a higher accuracy than a state-of-art network trained on the same set of images using binary labels. Further analyzing the results show that training a model using the image pairs learnt better aesthetic features than training on same number of individual binary labelled images.
Additionally, an attempt is made at enhancing the performance of the system by incorporating saliency related information. Given an image, humans might fixate their vision on particular parts of the image, which they might be subconsciously intrigued to. I therefore tried to utilize the saliency information both stand-alone as well as in combination with the global and local aesthetic features by performing two separate sets of experiments. In both the cases, a standard saliency model is chosen and the generated saliency maps are convoluted with the images prior to passing them to the network, thus giving higher importance to the salient regions as compared to the remaining. Thus generated saliency-images are either used independently or along with the global and the local features to train the network. Empirical results show that the saliency related aesthetic features might already be learnt by the network as a sub-set of the global features from automatic feature extraction, thus proving the redundancy of the additional saliency module.
ContributorsGattupalli, Jaya Vijetha (Author) / Li, Baoxin (Thesis advisor) / Davulcu, Hasan (Committee member) / Liang, Jianming (Committee member) / Arizona State University (Publisher)
Created2016
Description
Alzheimer’s disease (AD), is a chronic neurodegenerative disease that usually starts slowly and gets worse over time. It is the cause of 60% to 70% of cases of dementia. There is growing interest in identifying brain image biomarkers that help evaluate AD risk pre-symptomatically. High-dimensional non-linear pattern classification methods have been applied to structural magnetic resonance images (MRI’s) and used to discriminate between clinical groups in Alzheimers progression. Using Fluorodeoxyglucose (FDG) positron emission tomography (PET) as the pre- ferred imaging modality, this thesis develops two independent machine learning based patch analysis methods and uses them to perform six binary classification experiments across different (AD) diagnostic categories. Specifically, features were extracted and learned using dimensionality reduction and dictionary learning & sparse coding by taking overlapping patches in and around the cerebral cortex and using them as fea- tures. Using AdaBoost as the preferred choice of classifier both methods try to utilize 18F-FDG PET as a biological marker in the early diagnosis of Alzheimer’s . Addi- tional we investigate the involvement of rich demographic features (ApoeE3, ApoeE4 and Functional Activities Questionnaires (FAQ)) in classification. The experimental results on Alzheimer’s Disease Neuroimaging initiative (ADNI) dataset demonstrate the effectiveness of both the proposed systems. The use of 18F-FDG PET may offer a new sensitive biomarker and enrich the brain imaging analysis toolset for studying the diagnosis and prognosis of AD.
ContributorsSrivastava, Anant (Author) / Wang, Yalin (Thesis advisor) / Bansal, Ajay (Thesis advisor) / Liang, Jianming (Committee member) / Arizona State University (Publisher)
Created2017
Description
Alzheimer’s Disease (AD), a neurodegenerative disease is a progressive disease that affects the brain gradually with time and worsens. Reliable and early diagnosis of AD and its prodromal stages (i.e. Mild Cognitive Impairment(MCI)) is essential. Fluorodeoxyglucose (FDG) positron emission tomography (PET) measures the decline in the regional cerebral metabolic rate for glucose, offering a reliable metabolic biomarker even on presymptomatic AD patients. PET scans provide functional information that is unique and unavailable using other types of imaging. The computational efficacy of FDG-PET data alone, for the classification of various Alzheimer’s Diagnostic categories (AD, MCI (LMCI, EMCI), Control) has not been studied. This serves as motivation to correctly classify the various diagnostic categories using FDG-PET data. Deep learning has recently been applied to the analysis of structural and functional brain imaging data. This thesis is an introduction to a deep learning based classification technique using neural networks with dimensionality reduction techniques to classify the different stages of AD based on FDG-PET image analysis.
This thesis develops a classification method to investigate the performance of FDG-PET as an effective biomarker for Alzheimer's clinical group classification. This involves dimensionality reduction using Probabilistic Principal Component Analysis on max-pooled data and mean-pooled data, followed by a Multilayer Feed Forward Neural Network which performs binary classification. Max pooled features result into better classification performance compared to results on mean pooled features. Additionally, experiments are done to investigate if the addition of important demographic features such as Functional Activities Questionnaire(FAQ), gene information helps improve performance. Classification results indicate that our designed classifiers achieve competitive results, and better with the additional of demographic features.
This thesis develops a classification method to investigate the performance of FDG-PET as an effective biomarker for Alzheimer's clinical group classification. This involves dimensionality reduction using Probabilistic Principal Component Analysis on max-pooled data and mean-pooled data, followed by a Multilayer Feed Forward Neural Network which performs binary classification. Max pooled features result into better classification performance compared to results on mean pooled features. Additionally, experiments are done to investigate if the addition of important demographic features such as Functional Activities Questionnaire(FAQ), gene information helps improve performance. Classification results indicate that our designed classifiers achieve competitive results, and better with the additional of demographic features.
ContributorsSingh, Shibani (Author) / Wang, Yalin (Thesis advisor) / Li, Baoxin (Committee member) / Liang, Jianming (Committee member) / Arizona State University (Publisher)
Created2017
Description
Alzheimer's disease (AD) is a neurodegenerative disease that damages the cognitive abilities of a patient. It is critical to diagnose AD early to begin treatment as soon as possible which can be done through biomarkers. One such biomarker is the beta-amyloid (Aβ) peptide which can be quantified using the centiloid (CL) scale. For identifying the Aβ biomarker, A deep learning model that can model AD progression by predicting the CL value for brain magnetic resonance images (MRIs) is proposed. Brain MRI images can be obtained through the Alzheimer's Disease Neuroimaging Initiative (ADNI) and Open Access Series of Imaging Studies (OASIS) datasets, however a single model cannot perform well on both datasets at once. Thus, A regularization-based continuous learning framework to perform domain adaptation on the previous model is also proposed which captures the latent information about the relationship between Aβ and AD progression within both datasets.
ContributorsTrinh, Matthew Brian (Author) / Wang, Yalin (Thesis advisor) / Liang, Jianming (Committee member) / Su, Yi (Committee member) / Arizona State University (Publisher)
Created2022
Description
Insufficient training data poses significant challenges to training a deep convolutional neural network (CNN) to solve a target task. One common solution to this problem is to use transfer learning with pre-trained networks to apply knowledge learned from one domain with sufficient data to a new domain with limited data and avoid training a deep network from scratch. However, for such methods to work in a transfer learning setting, learned features from the source domain need to be generalizable to the target domain, which is not guaranteed since the feature space and distributions of the source and target data may be different. This thesis aims to explore and understand the use of orthogonal convolutional neural networks to improve learning of diverse, generic features that are transferable to a novel task.
In this thesis, orthogonal regularization is used to pre-train deep CNNs to investigate if and how orthogonal convolution may improve feature extraction in transfer learning. Experiments using two limited medical image datasets in this thesis suggests that orthogonal regularization improves generality and reduces redundancy of learned features more effectively in certain deep networks for transfer learning. The results on feature selection and classification demonstrate the improvement in transferred features helps select more expressive features that improves generalization performance. To understand the effectiveness of orthogonal regularization on different architectures, this work studies the effects of residual learning on orthogonal convolution. Specifically, this work examines the presence of residual connections and its effects on feature similarities and show residual learning blocks help orthogonal convolution better preserve feature diversity across convolutional layers of a network and alleviate the increase in feature similarities caused by depth, demonstrating the importance of residual learning in making orthogonal convolution more effective.
ContributorsChan, Tsz (Author) / Li, Baoxin (Thesis advisor) / Liang, Jianming (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2023