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- All Subjects: Computer Science
- Creators: Yang, Yezhou
Description
Rapid intraoperative diagnosis of brain tumors is of great importance for planning treatment and guiding the surgeon about the extent of resection. Currently, the standard for the preliminary intraoperative tissue analysis is frozen section biopsy that has major limitations such as tissue freezing and cutting artifacts, sampling errors, lack of immediate interaction between the pathologist and the surgeon, and time consuming.
Handheld, portable confocal laser endomicroscopy (CLE) is being explored in neurosurgery for its ability to image histopathological features of tissue at cellular resolution in real time during brain tumor surgery. Over the course of examination of the surgical tumor resection, hundreds to thousands of images may be collected. The high number of images requires significant time and storage load for subsequent reviewing, which motivated several research groups to employ deep convolutional neural networks (DCNNs) to improve its utility during surgery. DCNNs have proven to be useful in natural and medical image analysis tasks such as classification, object detection, and image segmentation.
This thesis proposes using DCNNs for analyzing CLE images of brain tumors. Particularly, it explores the practicality of DCNNs in three main tasks. First, off-the shelf DCNNs were used to classify images into diagnostic and non-diagnostic. Further experiments showed that both ensemble modeling and transfer learning improved the classifier’s accuracy in evaluating the diagnostic quality of new images at test stage. Second, a weakly-supervised learning pipeline was developed for localizing key features of diagnostic CLE images from gliomas. Third, image style transfer was used to improve the diagnostic quality of CLE images from glioma tumors by transforming the histology patterns in CLE images of fluorescein sodium-stained tissue into the ones in conventional hematoxylin and eosin-stained tissue slides.
These studies suggest that DCNNs are opted for analysis of CLE images. They may assist surgeons in sorting out the non-diagnostic images, highlighting the key regions and enhancing their appearance through pattern transformation in real time. With recent advances in deep learning such as generative adversarial networks and semi-supervised learning, new research directions need to be followed to discover more promises of DCNNs in CLE image analysis.
Handheld, portable confocal laser endomicroscopy (CLE) is being explored in neurosurgery for its ability to image histopathological features of tissue at cellular resolution in real time during brain tumor surgery. Over the course of examination of the surgical tumor resection, hundreds to thousands of images may be collected. The high number of images requires significant time and storage load for subsequent reviewing, which motivated several research groups to employ deep convolutional neural networks (DCNNs) to improve its utility during surgery. DCNNs have proven to be useful in natural and medical image analysis tasks such as classification, object detection, and image segmentation.
This thesis proposes using DCNNs for analyzing CLE images of brain tumors. Particularly, it explores the practicality of DCNNs in three main tasks. First, off-the shelf DCNNs were used to classify images into diagnostic and non-diagnostic. Further experiments showed that both ensemble modeling and transfer learning improved the classifier’s accuracy in evaluating the diagnostic quality of new images at test stage. Second, a weakly-supervised learning pipeline was developed for localizing key features of diagnostic CLE images from gliomas. Third, image style transfer was used to improve the diagnostic quality of CLE images from glioma tumors by transforming the histology patterns in CLE images of fluorescein sodium-stained tissue into the ones in conventional hematoxylin and eosin-stained tissue slides.
These studies suggest that DCNNs are opted for analysis of CLE images. They may assist surgeons in sorting out the non-diagnostic images, highlighting the key regions and enhancing their appearance through pattern transformation in real time. With recent advances in deep learning such as generative adversarial networks and semi-supervised learning, new research directions need to be followed to discover more promises of DCNNs in CLE image analysis.
ContributorsIzady Yazdanabadi, Mohammadhassan (Author) / Preul, Mark (Thesis advisor) / Yang, Yezhou (Thesis advisor) / Nakaji, Peter (Committee member) / Vernon, Brent (Committee member) / Arizona State University (Publisher)
Created2019
Description
Visual processing in social media platforms is a key step in gathering and understanding information in the era of Internet and big data. Online data is rich in content, but its processing faces many challenges including: varying scales for objects of interest, unreliable and/or missing labels, the inadequacy of single modal data and difficulty in analyzing high dimensional data. Towards facilitating the processing and understanding of online data, this dissertation primarily focuses on three challenges that I feel are of great practical importance: handling scale differences in computer vision tasks, such as facial component detection and face retrieval, developing efficient classifiers using partially labeled data and noisy data, and employing multi-modal models and feature selection to improve multi-view data analysis. For the first challenge, I propose a scale-insensitive algorithm to expedite and accurately detect facial landmarks. For the second challenge, I propose two algorithms that can be used to learn from partially labeled data and noisy data respectively. For the third challenge, I propose a new framework that incorporates feature selection modules into LDA models.
ContributorsZhou, Xu (Author) / Li, Baoxin (Thesis advisor) / Hsiao, Sharon (Committee member) / Davulcu, Hasan (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2018
Description
Students learn in various ways \u2014 visualization, auditory, memorizing, or making analogies. Traditional lecturing in engineering courses and the learning styles of engineering students are inharmonious causing students to be at a disadvantage based on their learning style (Felder & Silverman, 1988). My study analyzes the traditional approach to learning coding skills which is unnatural to engineering students with no previous exposure and examining if visual learning enhances introductory computer science education. Visual and text-based learning are evaluated to determine how students learn introductory coding skills and associated problem solving skills. My study was conducted to observe how the two types of learning aid the students in learning how to problem solve as well as how much knowledge can be obtained in a short period of time. The application used for visual learning was Scratch and Repl.it was used for text-based learning. Two exams were made to measure the progress made by each student. The topics covered by the exam were initialization, variable reassignment, output, if statements, if else statements, nested if statements, logical operators, arrays/lists, while loop, type casting, functions, object orientation, and sorting. Analysis of the data collected in the study allow us to observe whether the traditional method of teaching programming or block-based programming is more beneficial and in what topics of introductory computer science concepts.
ContributorsVidaure, Destiny Vanessa (Author) / Meuth, Ryan (Thesis director) / Yang, Yezhou (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
In this thesis, I propose a new technique of Aligning English sentence words
with its Semantic Representation using Inductive Logic Programming(ILP). My
work focusses on Abstract Meaning Representation(AMR). AMR is a semantic
formalism to English natural language. It encodes meaning of a sentence in a rooted
graph. This representation has gained attention for its simplicity and expressive power.
An AMR Aligner aligns words in a sentence to nodes(concepts) in its AMR
graph. As AMR annotation has no explicit alignment with words in English sentence,
automatic alignment becomes a requirement for training AMR parsers. The aligner in
this work comprises of two components. First, rules are learnt using ILP that invoke
AMR concepts from sentence-AMR graph pairs in the training data. Second, the
learnt rules are then used to align English sentences with AMR graphs. The technique
is evaluated on publicly available test dataset and the results are comparable with
state-of-the-art aligner.
with its Semantic Representation using Inductive Logic Programming(ILP). My
work focusses on Abstract Meaning Representation(AMR). AMR is a semantic
formalism to English natural language. It encodes meaning of a sentence in a rooted
graph. This representation has gained attention for its simplicity and expressive power.
An AMR Aligner aligns words in a sentence to nodes(concepts) in its AMR
graph. As AMR annotation has no explicit alignment with words in English sentence,
automatic alignment becomes a requirement for training AMR parsers. The aligner in
this work comprises of two components. First, rules are learnt using ILP that invoke
AMR concepts from sentence-AMR graph pairs in the training data. Second, the
learnt rules are then used to align English sentences with AMR graphs. The technique
is evaluated on publicly available test dataset and the results are comparable with
state-of-the-art aligner.
ContributorsAgarwal, Shubham (Author) / Baral, Chitta (Thesis advisor) / Li, Baoxin (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2017
Description
LPMLN is a recent probabilistic logic programming language which combines both Answer Set Programming (ASP) and Markov Logic. It is a proper extension of Answer Set programs which allows for reasoning about uncertainty using weighted rules under the stable model semantics with a weight scheme that is adopted from Markov Logic. LPMLN has been shown to be related to several formalisms from the knowledge representation (KR) side such as ASP and P-Log, and the statistical relational learning (SRL) side such as Markov Logic Networks (MLN), Problog and Pearl’s causal models (PCM). Formalisms like ASP, P-Log, Problog, MLN, PCM have all been shown to embeddable in LPMLN which demonstrates the expressivity of the language. Interestingly, LPMLN has also been shown to reducible to ASP and MLN which is not only theoretically interesting, but also practically important from a computational point of view in that the reductions yield ways to compute LPMLN programs utilizing ASP and MLN solvers. Additionally, the reductions also allow the users to compute other formalisms which can be reduced to LPMLN.
This thesis realizes two implementations of LPMLN based on the reductions from LPMLN to ASP and LPMLN to MLN. This thesis first presents an implementation of LPMLN called LPMLN2ASP that uses standard ASP solvers for computing MAP inference using weak constraints, and marginal and conditional probabilities using stable models enumeration. Next, in this thesis, another implementation of LPMLN called LPMLN2MLN is presented that uses MLN solvers which apply completion to compute the tight fragment of LPMLN programs for MAP inference, marginal and conditional probabilities. The computation using ASP solvers yields exact inference as opposed to approximate inference using MLN solvers. Using these implementations, the usefulness of LPMLN for computing other formalisms is demonstrated by reducing them to LPMLN. The thesis also shows how the implementations are better than the native solvers of some of these formalisms on certain domains. The implementations make use of the current state of the art solving technologies in ASP and MLN, and therefore they benefit from any theoretical and practical advances in these technologies, thereby also benefiting the computation of other formalisms that can be reduced to LPMLN. Furthermore, the implementation also allows for certain SRL formalisms to be computed by ASP solvers, and certain KR formalisms to be computed by MLN solvers.
This thesis realizes two implementations of LPMLN based on the reductions from LPMLN to ASP and LPMLN to MLN. This thesis first presents an implementation of LPMLN called LPMLN2ASP that uses standard ASP solvers for computing MAP inference using weak constraints, and marginal and conditional probabilities using stable models enumeration. Next, in this thesis, another implementation of LPMLN called LPMLN2MLN is presented that uses MLN solvers which apply completion to compute the tight fragment of LPMLN programs for MAP inference, marginal and conditional probabilities. The computation using ASP solvers yields exact inference as opposed to approximate inference using MLN solvers. Using these implementations, the usefulness of LPMLN for computing other formalisms is demonstrated by reducing them to LPMLN. The thesis also shows how the implementations are better than the native solvers of some of these formalisms on certain domains. The implementations make use of the current state of the art solving technologies in ASP and MLN, and therefore they benefit from any theoretical and practical advances in these technologies, thereby also benefiting the computation of other formalisms that can be reduced to LPMLN. Furthermore, the implementation also allows for certain SRL formalisms to be computed by ASP solvers, and certain KR formalisms to be computed by MLN solvers.
ContributorsTalsania, Samidh (Author) / Lee, Joohyung (Thesis advisor, Committee member) / Baral, Chitta (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2017
Description
Visual Question Answering (VQA) is a new research area involving technologies ranging from computer vision, natural language processing, to other sub-fields of artificial intelligence such as knowledge representation. The fundamental task is to take as input one image and one question (in text) related to the given image, and to generate a textual answer to the input question. There are two key research problems in VQA: image understanding and the question answering. My research mainly focuses on developing solutions to support solving these two problems.
In image understanding, one important research area is semantic segmentation, which takes images as input and output the label of each pixel. As much manual work is needed to label a useful training set, typical training sets for such supervised approaches are always small. There are also approaches with relaxed labeling requirement, called weakly supervised semantic segmentation, where only image-level labels are needed. With the development of social media, there are more and more user-uploaded images available
on-line. Such user-generated content often comes with labels like tags and may be coarsely labelled by various tools. To use these information for computer vision tasks, I propose a new graphic model by considering the neighborhood information and their interactions to obtain the pixel-level labels of the images with only incomplete image-level labels. The method was evaluated on both synthetic and real images.
In question answering, my research centers on best answer prediction, which addressed two main research topics: feature design and model construction. In the feature design part, most existing work discussed how to design effective features for answer quality / best answer prediction. However, little work mentioned how to design features by considering the relationship between answers of one given question. To fill this research gap, I designed new features to help improve the prediction performance. In the modeling part, to employ the structure of the feature space, I proposed an innovative learning-to-rank model by considering the hierarchical lasso. Experiments with comparison with the state-of-the-art in the best answer prediction literature have confirmed
that the proposed methods are effective and suitable for solving the research task.
In image understanding, one important research area is semantic segmentation, which takes images as input and output the label of each pixel. As much manual work is needed to label a useful training set, typical training sets for such supervised approaches are always small. There are also approaches with relaxed labeling requirement, called weakly supervised semantic segmentation, where only image-level labels are needed. With the development of social media, there are more and more user-uploaded images available
on-line. Such user-generated content often comes with labels like tags and may be coarsely labelled by various tools. To use these information for computer vision tasks, I propose a new graphic model by considering the neighborhood information and their interactions to obtain the pixel-level labels of the images with only incomplete image-level labels. The method was evaluated on both synthetic and real images.
In question answering, my research centers on best answer prediction, which addressed two main research topics: feature design and model construction. In the feature design part, most existing work discussed how to design effective features for answer quality / best answer prediction. However, little work mentioned how to design features by considering the relationship between answers of one given question. To fill this research gap, I designed new features to help improve the prediction performance. In the modeling part, to employ the structure of the feature space, I proposed an innovative learning-to-rank model by considering the hierarchical lasso. Experiments with comparison with the state-of-the-art in the best answer prediction literature have confirmed
that the proposed methods are effective and suitable for solving the research task.
ContributorsTian, Qiongjie (Author) / Li, Baoxin (Thesis advisor) / Tong, Hanghang (Committee member) / Davulcu, Hasan (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2017
Description
Compressive sensing theory allows to sense and reconstruct signals/images with lower sampling rate than Nyquist rate. Applications in resource constrained environment stand to benefit from this theory, opening up many possibilities for new applications at the same time. The traditional inference pipeline for computer vision sequence reconstructing the image from compressive measurements. However,the reconstruction process is a computationally expensive step that also provides poor results at high compression rate. There have been several successful attempts to perform inference tasks directly on compressive measurements such as activity recognition. In this thesis, I am interested to tackle a more challenging vision problem - Visual question answering (VQA) without reconstructing the compressive images. I investigate the feasibility of this problem with a series of experiments, and I evaluate proposed methods on a VQA dataset and discuss promising results and direction for future work.
ContributorsHuang, Li-Chin (Author) / Turaga, Pavan (Thesis advisor) / Yang, Yezhou (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2017
Description
In recent years, several methods have been proposed to encode sentences into fixed length continuous vectors called sentence representation or sentence embedding. With the recent advancements in various deep learning methods applied in Natural Language Processing (NLP), these representations play a crucial role in tasks such as named entity recognition, question answering and sentence classification.
Traditionally, sentence vector representations are learnt from its constituent word representations, also known as word embeddings. Various methods to learn the distributed representation (embedding) of words have been proposed using the notion of Distributional Semantics, i.e. “meaning of a word is characterized by the company it keeps”. However, principle of compositionality states that meaning of a sentence is a function of the meanings of words and also the way they are syntactically combined. In various recent methods for sentence representation, the syntactic information like dependency or relation between words have been largely ignored.
In this work, I have explored the effectiveness of sentence representations that are composed of the representation of both, its constituent words and the relations between the words in a sentence. The word and relation embeddings are learned based on their context. These general-purpose embeddings can also be used as off-the- shelf semantic and syntactic features for various NLP tasks. Similarity Evaluation tasks was performed on two datasets showing the usefulness of the learned word embeddings. Experiments were conducted on three different sentence classification tasks showing that our sentence representations outperform the original word-based sentence representations, when used with the state-of-the-art Neural Network architectures.
Traditionally, sentence vector representations are learnt from its constituent word representations, also known as word embeddings. Various methods to learn the distributed representation (embedding) of words have been proposed using the notion of Distributional Semantics, i.e. “meaning of a word is characterized by the company it keeps”. However, principle of compositionality states that meaning of a sentence is a function of the meanings of words and also the way they are syntactically combined. In various recent methods for sentence representation, the syntactic information like dependency or relation between words have been largely ignored.
In this work, I have explored the effectiveness of sentence representations that are composed of the representation of both, its constituent words and the relations between the words in a sentence. The word and relation embeddings are learned based on their context. These general-purpose embeddings can also be used as off-the- shelf semantic and syntactic features for various NLP tasks. Similarity Evaluation tasks was performed on two datasets showing the usefulness of the learned word embeddings. Experiments were conducted on three different sentence classification tasks showing that our sentence representations outperform the original word-based sentence representations, when used with the state-of-the-art Neural Network architectures.
ContributorsRath, Trideep (Author) / Baral, Chitta (Thesis advisor) / Li, Baoxin (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2017
Description
Graph matching is a fundamental but notoriously difficult problem due to its NP-hard nature, and serves as a cornerstone for a series of applications in machine learning and computer vision, such as image matching, dynamic routing, drug design, to name a few. Although there has been massive previous investigation on high-performance graph matching solvers, it still remains a challenging task to tackle the matching problem under real-world scenarios with severe graph uncertainty (e.g., noise, outlier, misleading or ambiguous link).In this dissertation, a main focus is to investigate the essence and propose solutions to graph matching with higher reliability under such uncertainty. To this end, the proposed research was conducted taking into account three perspectives related to reliable graph matching: modeling, optimization and learning. For modeling, graph matching is extended from typical quadratic assignment problem to a more generic mathematical model by introducing a specific family of separable function, achieving higher capacity and reliability. In terms of optimization, a novel high gradient-efficient determinant-based regularization technique is proposed in this research, showing high robustness against outliers. Then learning paradigm for graph matching under intrinsic combinatorial characteristics is explored. First, a study is conducted on the way of filling the gap between discrete problem and its continuous approximation under a deep learning framework. Then this dissertation continues to investigate the necessity of more reliable latent topology of graphs for matching, and propose an effective and flexible framework to obtain it. Coherent findings in this dissertation include theoretical study and several novel algorithms, with rich experiments demonstrating the effectiveness.
ContributorsYu, Tianshu (Author) / Li, Baoxin (Thesis advisor) / Wang, Yalin (Committee member) / Yang, Yezhou (Committee member) / Yang, Yingzhen (Committee member) / Arizona State University (Publisher)
Created2021
Description
Graph matching is a fundamental but notoriously difficult problem due to its NP-hard nature, and serves as a cornerstone for a series of applications in machine learning and computer vision, such as image matching, dynamic routing, drug design, to name a few. Although there has been massive previous investigation on high-performance graph matching solvers, it still remains a challenging task to tackle the matching problem under real-world scenarios with severe graph uncertainty (e.g., noise, outlier, misleading or ambiguous link).In this dissertation, a main focus is to investigate the essence and propose solutions to graph matching with higher reliability under such uncertainty. To this end, the proposed research was conducted taking into account three perspectives related to reliable graph matching: modeling, optimization and learning. For modeling, graph matching is extended from typical quadratic assignment problem to a more generic mathematical model by introducing a specific family of separable function, achieving higher capacity and reliability. In terms of optimization, a novel high gradient-efficient determinant-based regularization technique is proposed in this research, showing high robustness against outliers. Then learning paradigm for graph matching under intrinsic combinatorial characteristics is explored. First, a study is conducted on the way of filling the gap between discrete problem and its continuous approximation under a deep learning framework. Then this dissertation continues to investigate the necessity of more reliable latent topology of graphs for matching, and propose an effective and flexible framework to obtain it. Coherent findings in this dissertation include theoretical study and several novel algorithms, with rich experiments demonstrating the effectiveness.
ContributorsYu, Tianshu (Author) / Li, Baoxin (Thesis advisor) / Wang, Yalin (Committee member) / Yang, Yezhou (Committee member) / Yang, Yingzhen (Committee member) / Arizona State University (Publisher)
Created2021