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Title: DEEP LEARNING FOR IMAGE PROCESSING WITH APPLICATIONS TO MEDICAL IMAGING
Creator: Zarshenas, Amin
Date: 2019
Description: Deep Learning is a subfield of machine learning concerned with algorithms that learn hierarchical data representations. Deep learning has...
Show moreDeep Learning is a subfield of machine learning concerned with algorithms that learn hierarchical data representations. Deep learning has proven extremely successful in many computer vision tasks including object detection and recognition. In this thesis, we aim to develop and design deep-learning models to better perform image processing and tackle three important problems: natural image denoising, computed tomography (CT) dose reduction, and bone suppression in chest radiography (“chest x-ray”: CXR). As the first contribution of this thesis, we aimed to answer to probably the most critical design questions, under the task of natural image denoising. To this end, we defined a class of deep learning models, called neural network convolution (NNC). We investigated several design modules for designing NNC for image processing. Based on our analysis, we design a deep residual NNC (R-NNC) for this task. One of the important challenges in image denoising regards to a scenario in which the images have varying noise levels. Our analysis showed that training a single R-NNC on images at multiple noise levels results in a network that cannot handle very high noise levels; and sometimes, it blurs the high-frequency information on less noisy areas. To address this problem, we designed and developed two new deep-learning structures, namely, noise-specific NNC (NS-NNC) and a DeepFloat model, for the task of image denoising at varying noise levels. Our models achieved the highest denoising performance comparing to the state-of-the-art techniques.As the second contribution of the thesis, we aimed to tackle the task of CT dose reduction by means of our NNC. Studies have shown that high dose of CT scans can increase the risk of radiation-induced cancer in patients dramatically; therefore, it is very important to reduce the radiation dose as much as possible. For this problem, we introduced a mixture of anatomy-specific (AS) NNC experts. The basic idea is to train multiple NNC models for different anatomic segments with different characteristics, and merge the predictions based on the segmentations. Our phantom and clinical analysis showed that more than 90% dose reduction would be achieved using our AS NNC model.We exploited our findings from image denoising and CT dose reduction, to tackle the challenging task of bone suppression in CXRs. Most lung nodules that are missed by radiologists as well as by computer-aided detection systems overlap with bones in CXRs. Our purpose was to develop an imaging system to virtually separate ribs and clavicles from lung nodules and soft-tissue in CXRs. To achieve this, we developed a mixture of anatomy-specific, orientation-frequency-specific (ASOFS) expert deep NNC model. While our model was able to decompose the CXRs, to achieve an even higher bone suppression performance, we employed our deep R-NNC for the bone suppression application. Our model was able to create bone and soft-tissue images from single CXRs, without requiring specialized equipment or increasing the radiation dose.
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Title: ANALYZING THE LINGUISTIC CHARACTERISTICS OF MARIJUANA USE BY INCOME USING SOCIAL MEDIA
Creator: Zeinali, Sahand
Date: 2018, 2018-05
Description: Marijuana use and legality has been a widely-discussed topic in the recent years. Knowing that marijuana has different effects on health, mood...
Show moreMarijuana use and legality has been a widely-discussed topic in the recent years. Knowing that marijuana has different effects on health, mood and behavior after its use, it is important to understand what the underlying causes for marijuana use also are. As marijuana use is becoming more prevalent every day, it is crucial to know what the motives behind the users' tendencies are for smoking marijuana. To be able to identify the words/patterns associated with marijuana use prior to its use, we will need a real-time method to understand the problem on a deeper level with a better method than surveying users. In our study, we aim to understand the different linguistic characteristics of marijuana users based on their income. Social media's provision of data into understanding and tracking people's behavior can be very beneficial in understanding the contrast between the different social classes prior to marijuana use and understand what the underlying causes are for their marijuana use. In our experiment, we use social media to analyze the patterns and characteristics of marijuana use based on income class. By collecting data on Twitter, we then proceed to classify users based on their income. Using this method, we predict the income of each user by utilizing the user's Twitter activity and their linguistic characteristics based on the tweets associated with them. Through the experiment, we can identify patterns amongst the marijuana users in two different income classes and predict what class a user will be placed in based on their recent Twitter activity with a good accuracy.
M.S. in Computer Science, May 2018
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Title: ACTIVE INFERENCE FOR PREDICTIVE MODELS OF SPATIO-TEMPORAL DOMAINS
Creator: Komurlu, Caner
Date: 2019
Description: Active inference is the method of selective information gathering during prediction in order to increase a predictive machine learning model's...
Show moreActive inference is the method of selective information gathering during prediction in order to increase a predictive machine learning model's prediction performance. Unlike active learning, active inference does not update the model, but rather provides the model with useful information during prediction to boost the prediction performance. To be able to work with active inference, a predictive model needs to exploit correlations among variables that need to be predicted. Then the model, while being provided with true values for some of the variables, can make more accurate predictions for the remaining variables.In this dissertation, I propose active inference methods for predictive models of spatio-temporal domains. I formulate and investigate active inference in two different domains: tissue engineering and wireless sensor networks. I develop active inference for dynamic Bayesian networks (DBNs) and feed-forward neural networks (FFNNs).First, I explore the effect of active inference in the tissue engineering domain. I design a dynamic Bayesian network (DBN) model for vascularization of a tissue development site. The DBN model predicts probabilities of blood vessel invasion in regional scale through time. Then utilizing spatio-temporal correlations between regions represented as variables in the DBN model, I develop an active inference technique to detect the optimal time to stop a wet lab experiment. The empirical study shows that the active inference is able to detect the optimal time and the results are coherent with domain simulations and lab experiments.In the second phase of my research, I develop variance-based active inference techniques for dynamic Bayesian networks for the purpose of battery saving for wireless sensor networks (WSN). I propose the expected variance reduction active inference method to detect variables that reduce the overall variance the most. I first propose a DBN model of a WSN. I then compare the prediction performance of the DBN with Gaussian processes and linear chain graphical models on three different WSN data using several baseline active inference methods. After showing that DBNs perform better than the baseline predictive models, I compare the performance of expected variance reduction active inference method with the performances of baseline methods on the DBN, and show the superiority of the expected variance reduction on the three WSN data sets.Finally, to address the inference complexity and the limitation of representing linear correlations due to Gaussian assumption, I replace the DBN representation with a feed-forward neural network (FFNN) model. I first explore techniques to integrate observed values into predictions on neural networks. I adopt the input optimization technique. Finally, I discover two problems: model error and optimization overfitting. I show that the input optimization can mitigate the model error. Lastly, I propose a validation-based regularization approach to solve the overfitting problem.
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Title: Fast mesh based reconstruction for cardiac-gated SPECT and methodology for medical image quality assessment
Creator: Massanes Basi, Francesc
Date: 2018
Description: In this work, we are studying two different subjects that are intricately connected. For the first subject we are considering tools to...
Show moreIn this work, we are studying two different subjects that are intricately connected. For the first subject we are considering tools to improve the quality of single photon emission computed tomography (SPECT) imaging. Currently, SPECT images assist physicians to evaluate perfusion levels within the myocardium, aide in the diagnosis of various types of carcinomas, and measure pulmonary function. The SPECT technique relies on injecting a radioactive material into the patient's body and then detecting the emitted radiation by means of a gamma camera. However, the amount of radioactive material that can be given to a patient is limited by the negative effects that the radiation will have on the patient's health. This causes SPECT images to be highly corrupted by noise. We will focus our work on cardiac SPECT, which adds the challenge of the heart's continuous motion during the acquisition process. First, we describe the methodology used in SPECT imaging and reconstruction. Our methodology uses a content adaptive model, which uses more samples on the regions of the body that we want to be reconstructed more accurately and less in other areas. Then we describe our algorithm and our novel implementation that lets us use the content adaptive model to perform the reconstruction. In this work, we show that our implementation outperforms the reconstruction method used for clinical applications. In the second subject we are evaluating tools to measure image quality in the context of medical diagnosis. In signal processing, accuracy is typically measured as the amount of similarity between an original signal and its reconstruction. This similarity is traditionally a numeric metric that does not take into account the intended purpose of the reconstructed images. In the field of medical imaging, a reconstructed image is meant to aid a physician to perform a diagnostic task. Therefore, the quality of the reconstruction should be measured by how much it helps to perform the diagnostic task. A model observer is a computer tool that aims to mimic the performance of human observer, usually a radiologist, at a relevant diagnosis task. In this work we present our linear model observer designed to automatically select the features needed to model a human observer response. This is a novelty from the model observers currently being used in the medical imaging field, which instead usually have ad-hoc chosen features. Our model observer dependents only on the resolution of the image, not the type of imaging technique used to acquire the image.
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Title: PRIVACY PRESERVING BAG PREPARATION FOR LEARNING FROM LABEL PROPORTION
Creator: Yan, Xinzhou
Date: 2018
Description: We apply Privacy-preserving data mining standards (PPDM) to the Learning from label proportion (LLP) model to create the Private-preserving...
Show moreWe apply Privacy-preserving data mining standards (PPDM) to the Learning from label proportion (LLP) model to create the Private-preserving machine learning framework. We design the data preparation step for the LLP framework to meet the PPDM standards. In the data preparation step, we develop a bag selection method to boost the accuracy of the LLP model by more than 7%. Besides that, we propose three K- anonymous aggregation methods for the datasets which have almost zero accuracy loss and very robust. After the K-anonymous step, we apply Differential privacy to the LLP model and ensure a low accuracy loss for the LLP modelBecause of the LLP model’s special loss function, not only it is possible to replace all the feature vectors with the mean feature vector within each bag, but also the accuracy loss caused by Differential privacy can be bounded by a small number. The loss function ensures low accuracy loss when training LLP model on PPDM dataset. We evaluate the PPDM LLP model on two datasets, one is the Adult dataset and the other is the Instagram comment dataset. Both of them give empirical evidence of the low accuracy loss after applying the PPDM LLP model.
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Title: A Complete Machine Learning Approach for Predicting Lithium-Ion Cell Combustion
Creator: Almagro Yravedra, Fernando
Date: 2020
Description: The object of the herein thesis work document is to develop a functional predictive model, able to predict the combustion of a US18650 Sony...
Show moreThe object of the herein thesis work document is to develop a functional predictive model, able to predict the combustion of a US18650 Sony Lithium-Ion cell given its current and previous states. In order to build the model, a realistic electro-thermal model of the cell under study is developed in Matlab Simulink, being used to recreate the cell's behavior under a set of real operating conditions. The data generated by the electro-thermal model is used to train a recurrent neural network, which returns the chance of future combustion of the US18650 Sony Lithium-Ion cell. Independently obtained data is used to test and validate the developed recurrent neural network using advanced metrics.
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Title: Public Event Identification Traffic Data Using Machine Learning Approach
Creator: Yang, Hanyi
Date: 2020
Description: This study developed a shock waved diagram based deep learning model (SW-DLM) to predict the occurrence of public events in real-time...
Show moreThis study developed a shock waved diagram based deep learning model (SW-DLM) to predict the occurrence of public events in real-time according to their impacts on nearby highway traffic. Specifically, using point traffic volume data as a boundary condition, shock wave analysis is first conducted to understand the impacts and features of a public event on a nearby highway-ramp intersection. Next, this analysis develops the SWG algorithm to efficiently generate and expand shock wave diagrams in real-time according to the data collection rate. Built upon that, this study contributes a novel approach, which encodes a shock wave diagram with an optimal grid of pixels balancing resolution and computation load. Using the features extracted from encoded time-series shock wave diagrams as inputs, a deep learning approach, Long-short term memory (LSTM) model, is applied to predict the occurring of a public event. The numerical experiments based on the field data demonstrate that using encoded shock wave diagrams rather than point traffic data can significantly improve the accuracy of the deep learning for predicting the occurring of a public event. The SW-DLM presents satisfied prediction performance on the average as well as on an individual day with or without traffic accident interference, happening nearby the venue of a public event. The implementation of this approach to real-time traffic provision tools such as GPS will alert travelers en route on-going events in a transportation network and help travelers to make a smart trip plan and avoid traffic congestion. Moreover, it promotes smart city development by providing a strong capability to monitor the transportation system and conduct real-time traffic management intelligently.
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Title: Reconfigurable High-Performance Computation and Communication Platform for Ultrasonic Applications
Creator: Wang, Boyang
Date: 2021
Description: In industrial and medical applications, ultrasonic signals are used in nondestructive testing (NDT), medical imaging, navigation, and...
Show moreIn industrial and medical applications, ultrasonic signals are used in nondestructive testing (NDT), medical imaging, navigation, and communication. This study presents the architecture of high-performance computational systems designed for ultrasonic nondestructive testing, data compression using machine learning, and a multilayer perceptron neural network for ultrasonic flaw detection and grain size characterization. We researched and developed a real-time software-defined ultrasonic communication system for transmitting information through highly reverberant and dispersive solid channels. Orthogonal frequency-division multiplexing is explored to combat the severe multipath effect in the solid channels and achieve an optimal bitrate solution. In this study, a reconfigurable, high-performance, low-cost, and real-time ultrasonic data acquisition and signal processing platform is designed based on an all-programmable system-on-chip (APSoC). We designed the unsupervised learning models using wavelet packet transformation optimized by convolutional autoencoder for massive ultrasonic data compression. The proposed learning models can achieve a compression accuracy of 98% by using only 6% of the original data. For ultrasonic signal analysis in NDT applications, we utilized the multilayer perceptron neural network (MLPNN) to detect flaw echoes masked by strong microstructure scattering noise (i.e., about zero dB SNR or less) with detection accuracy above 99%. It is of high interest to characterize materials using ultrasonic scattering properties for grain size estimation and classification. We successfully designed an MLPNN to classify the grain sizes of materials with an accuracy of 99%. Furthermore, a software-defined ultrasonic communication system based on the APSoC is designed for real-time data transmission through solid channels. Transducers with a center frequency of 2.5 MHz are used to transmit and receive information-bearing ultrasonic waves in solid channels where the communication bit rate can reach up to 1.5 Mbps.
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Title: AUTOMATION OF ULTRASONIC FLAW DETECTION APPLICATIONS USING DEEP LEARNING ALGORITHMS
Creator: Virupakshappa, Kushal
Date: 2021
Description: The Industrial Revolution-4.0 promises to integrate multiple technologies including but not limited to automation, cloud computing, robotics,...
Show moreThe Industrial Revolution-4.0 promises to integrate multiple technologies including but not limited to automation, cloud computing, robotics, and Artificial Intelligence. The non-Destructive Testing (NDT) industry has been shifting towards automation as well. For ultrasound-based NDT, these technological advancements facilitate smart systems hosting complex signal processing algorithms. Therefore, this thesis introduces the effective use of AI algorithms in challenging NDT scenarios. The first objective is to investigate and evaluate the performance of both supervised and unsupervised machine learning algorithms and optimize them for ultrasonic flaw detection utilizing Amplitude-scan (A-scan) data. Several inferences and optimization algorithms have been evaluated. It has been observed that proper choice of features for specific inference algorithms leads to accurate flaw detection. The second objective of this study is the hardware realization of the ultrasonic flaw detection algorithms on embedded systems. Support Vector Machine algorithm has been implemented on a Tegra K1 GPU platform and Supervised Machine Learning algorithms have been implemented on a Zynq FPGA for a comparative study. The third main objective is to introduce new deep learning architectures for more complex flaw detection applications including classification of flaw types and robust detection of multiple flaws in B-scan data. The proposed Deep Learning pipeline combines a novel grid-based localization architecture with meta-learning. This provides a generalized flaw detection solution wherein additional flaw types can be used for inference without retraining or changing the deep learning architecture. Results show that the proposed algorithm performs well in more complex scenarios with high clutter noise and the results are comparable with traditional CNN and achieve the goal of generality and robustness.
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Title: DEVELOPMENT OF BIOMARKERS OF SMALL VESSEL DISEASE IN AGING
Creator: Makkinejad, Nazanin
Date: 2021
Description: Age-related neuropathologies including cerebrovascular and neurodegenerative diseases play a critical role in cognitive dysfunction, and...
Show moreAge-related neuropathologies including cerebrovascular and neurodegenerative diseases play a critical role in cognitive dysfunction, and development of dementia. Designing methodologies for early prediction of these diseases are much needed. Since multiple pathologies commonly coexist in brains of older adults, clinical diagnosis lacks the specificity to isolate the pathology of interest, and gold standard is determined only at autopsy. Magnetic resonance imaging (MRI) provides a non-invasive tool to study abnormalities in brain characteristics that is unique to each pathology. Utilizing ex-vivo MRI for brain imaging proves to be useful as it eliminates two important biases of in-vivo MRI. First, no additional pathology would develop between imaging and pathologic examination, and second, frail older adults would not be excluded from MRI.Hence, the aims of this dissertation were two-fold: to study brain correlates of age- related neuropathologies, and to develop and validate classifiers of small vessel diseases by combining ex-vivo MRI and pathology in a large community cohort of older adults. The structure of the project is as follows.First, the association of amygdala volume and shape with transactive response DNA-binding protein 43 (TDP-43) pathology was investigated. Using a regularized regression technique, higher TDP-43 was associated with lower amygdala volume. Also, shape analysis of amygdala showed unique patterns of spatial atrophy associated with TDP-43 independent of other pathologies. Lastly, using linear mixed effect models, amygdala volume was shown to explain an additional portion of variance in cognitive decline above and beyond what was explained by the neuropathologies and demographics.Second, the previous study was extended to analyze other subcortical regions including the hippocampus, thalamus, nucleus accumbens, caudate, and putamen, and was also conducted in a larger dataset. The results showed unique contribution of TDP-43, neurofibrillary tangles (hallmark characteristic of Alzheimer’s disease pathology), and atherosclerosis (a cerebrovascular pathology) to atrophy on the surface of subcortical structures. Understanding the independent effects of each pathology on volume and shape of different brain regions can form a basis for the development of classifiers of age-related neuropathologies.Third, an in-vivo classifier of arteriolosclerosis was developed and validated. Arteriolosclerosis is one of the main pathologies of small vessel disease, is associated with cognitive decline and dementia, and currently has no standard biomarker available. In this work, the classifier was developed ex-vivo using machine learning (ML) techniques and was then translated to in-vivo. The in-vivo classifier was packaged as a software called ARTS, which outputs a score that is the likelihood of arteriolosclerosis when the required input is given to the software. It was tested and validated in various cohorts and showed to have high performance in predicting the pathology. It was also shown that higher ARTS score was associated with greater cognitive decline in domains that are specific to small vessel disease.Fourth, motivated by current trends and superiority of deep learning (DL) techniques in classification tasks in computer vision and medical imaging, a preliminary study was designed to use DL for training an ex-vivo classifier of arteriolosclerosis. Specifically, convolutional neural networks (CNNs) were applied on 3 Tesla ex-vivo MR images directly without providing prior information of brain correlates of arteriolosclerosis. One interesting aspect of the results was that the network learnt that white matter hyperintense lesions contributed the most to classification of arteriolosclerosis. These results were encouraging, and more future work will exploit the capability of DL techniques alongside the traditional ML approaches for more automation and possibly better performance.Finally, a preliminary classifier of arteriolosclerosis and small vessel atherosclerosis was developed since the existence of both pathologies in brain have devastating effects on cognition. The methodology was similar to the one used for development of arteriolosclerosis classifier with minor differences. The classifier showed a good performance in-vivo, although the testing needs to be assessed in more cohorts.The comprehensive study of age-related neuropathologies and their contribution to abnormalities of subcortical brain structures offers a great potential to develop a biomarker of each pathology. Also, the finding that the MR-based classifier of arteriolosclerosis showed high performance in-vivo demonstrate the potential of ex-vivo studies for development of biomarkers that are precise (because they are based on autopsy, which is the gold standard) and are expected to work well in-vivo. The implications of this study include development of biomarkers that could potentially be used in refined participant selection and enhanced monitoring of the treatment response in clinical drug and prevention trials.
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Title: Towards Assisting Human-Human Conversations
Creator: Nanaware, Tejas Suryakant
Date: 2021
Description: The idea of the research is to understand the open-topic conversations and ways to provide assistance to humans who face difficulties in...
Show moreThe idea of the research is to understand the open-topic conversations and ways to provide assistance to humans who face difficulties in initiating conversations and overcome social anxiety so as to be able to talk and have successful conversations. By providing humans with assistive conversational support, we can augment the conversation that can be carried out. The AdvisorBot can also help to reduce the time taken to type and convey the message if the AdvisorBot is context aware and capable of providing good responses.There has been a significant research for creating conversational chatbots in open-domain conversations that have claimed to have passed the Turing Test and can converse with humans while not seeming like a bot. However, if these chatbots can converse like humans, can they provide actual assistance in human conversations? This research study observes and improves the advanced open-domain conversational chatbots that are put in practice for providing conversational assistance.While performing this thesis research, the chatbots were deployed to provide conversational assistance and a human study was performed to identify and improve the ways to tackle social anxiety by connecting strangers to perform conversations that would be aided by AdvisorBot. Through the questionnaires that the research subjects filled during their participation, and by performing linguistic analysis, the quality of the AdvisorBot can be improved so that humans can achieve better conversational skills and are able to clearly convey their message while conversing. The results were further enhanced by using transfer learning techniques and quickly improve the quality of the AdvisorBot.
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Title: UTILITY OF WATERSHED MODELS: IMPROVING TMDL DEVELOPMENT THROUGH A MARGIN OF SAFETY ESTIMATION AND UNCERTAINTY COMMUNICATION
Creator: Nunoo, Robert
Date: 2020
Description: Watershed models are used to represent the physical, chemical, and biological mechanisms that determine the fate and transport of pollutants...
Show moreWatershed models are used to represent the physical, chemical, and biological mechanisms that determine the fate and transport of pollutants in waterbodies (Daniel 2011). These models, in general, are used for exploratory, planning, and regulatory purposes (Harmel et al. 2014). Watershed models have numerous applications; one such use is the development of total maximum daily load (TMDL). TMDL is the amount of pollution a waterbody can receive without becoming impaired. Because of the challenge of uncertainty associated with models and the TMDL development process, the United States Clean Water Act Section 303 (d)(1)(c) requires that a margin of safety (MOS) be specified to account for uncertainty in TMDLs. The question of how MOS is estimated in TMDL was identified as a problem by the National Research Council (NRC 2001). Since the identification of the problem about two decades ago, there have been very few inventories or audits of approved TMDL studies. This study describes a natural language processing and machine learning aided review of the MOS in approved TMDLs from 2002 to 2016. The study determined whether the MOS values incorporated followed a pattern and examined whether there exist a relationship between MOS values and some ecological conditions. Relatively few TMDLs were based on some form of calculation to estimate explicit MOS values; these TMDLs constituted only 16% of the reviewed sample. The remaining 84% used conventional values, but few of those studies provided reasons for their selected values. A statistical assessment of those MOS values revealed that the MOS depended on States (location of waterbody), USEPA regions, waterbody type, designated water use, TMDL model used, and dataavailability. The findings indicate that few TMDL developers are following the National Research Council’s suggestions of using a rigorous uncertainty estimation approach for rational choices for the MOS. An adaptive approach based on Bayes-Discrepancy was proposed for estimating an MOS for a TMDL. The approach is based on the Bayesian hierarchical framework of estimating uncertainty associated with watershed models. With this approach, TMDL developers can communicate the effects of their watershed model. The approach was applied to a Ferson Creek model of the Fox River watershed to access variability and uncertainty in the model results, and also estimate possible MOS values for two monitoring stations in the watershed. Results suggest that an MOS of 0.04 mg/L could lead to a 0.1 probability of violating the water quality standard for an underpredicting model. The Bayes-discrepancy estimation method will enable TMDL developers and watershed managers to strike a balance between implementation options and water quality concerns.
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Title: A SCALABLE SIMULATION AND MODELING FRAMEWORK FOR EVALUATION OF SOFTWARE-DEFINED NETWORKING DESIGN AND SECURITY APPLICATIONS
Creator: Yan, Jiaqi
Date: 2019
Description: The world today is densely connected by many large-scale computer networks, supporting military applications, social communications, power...
Show moreThe world today is densely connected by many large-scale computer networks, supporting military applications, social communications, power grid facilities, cloud services, and other critical infrastructures. However, a gap has grown between the complexity of the system and the increasing need for security and resilience. We believe this gap is now reaching a tipping point, resulting in a dramatic change in the way that networks and applications are architected, developed, monitored, and protected. This trend calls for a scalable and high-fidelity network testing and evaluation platform to facilitate the transformation from in-house research ideas to real-world working solutions. With this objective, we investigate means to build a scalable and high-fidelity network testbed using container-based emulation and parallel simulation; our study focuses on the emerging software-defined networking (SDN) technology. Existing evaluation platforms facilitate the adoption of the SDN architecture and applications to production systems. However, the performance of those platforms is highly dependent on the underlying physical hardware resources. Insufficient resources would lead to undesired results, such as low experimental fidelity or slow execution speed, especially with large-scale network settings. To improve the testbed fidelity, we first develop a lightweight virtual time system for Linux container and integrate the system into a widely-used SDN emulator. A key issue with an ordinary container-based emulator is that it uses the system clock across all the containers even if a container is not being scheduled to run, which leads to the issue of both performance and temporal fidelity, especially with high workloads. We investigate virtual time approaches by precisely scaling the time of interactions between containers and physical devices. Our evaluation results indicate a definite improvement in fidelity and scalability. To improve the testbed scalability, we investigate how the centralized paradigm of SDN can be utilized to reduce the simulation workload. We explore a model abstraction technique that effectively transforms the SDN network devices to one virtualized switch model. While significantly reducing the model execution time and enabling the real-time simulation capability, our abstracted model also preserves the end-to-end forwarding behavior of the original network.With enhanced fidelity and scalability, it is realistic to utilize our network testbed to perform a security evaluation of various SDN applications. We notice that the communication network generates and processes a huge amount of data. The logically-centralized SDN control plane, on the one hand, has to process both critical control traffic and potentially big data traffic, and on the other hand, enables many efficient security solutions, such as intrusion detection, mitigation, and prevention. Recently, deep neural networks achieve state-of-the-art results across a range of hard problem spaces. We study how to utilize the big data and deep learning to secure communication networks and host entities. For classifying malicious network traffic, we have performed the feasibility study of off-line deep-learning based intrusion detection by constructing the detection engine with multiple advanced deep learning models. For malware classification on individual hosts, another necessity to secure computer systems, existing machine learning-based malware classification methods rely on handcrafted features extracted from raw binary files or disassembled code. The diversity of such features created has made it hard to build generic malware classification systems that work effectively across different operational environments. To strike a balance between generality and performance, we explore new graph convolutional neural network techniques to effectively yet efficiently classify malware programs represented as their control flow graphs.
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Title: Effect of Pre-Processing Data on Fairness and Fairness Debugging using GOPHER
Creator: Sarkar, Mousam
Date: 2023
Description: At present, Artificial intelligence has been contributing to the decision-making process heavily. Bias in machine learning models has existed...
Show moreAt present, Artificial intelligence has been contributing to the decision-making process heavily. Bias in machine learning models has existed throughout and present studies’ direct usage of eXplainable Artificial Intelligence (XAI) approaches to identify and study bias. To solve the problem of locating bias and then mitigating it has been achieved by Gopher [1]. It generates interpretable top-k explanations for the unfairness of the model and it also identifies subsets of training data that are the root cause of this unfair behavior. We utilize this system to study the effect of pre-processing on bias through provenance. The concept of data lineage through tagging of data points during and after the pre-processing stage is implemented. Our methodology and results provide a useful point of reference for studying the relation of pre-processing data with the unfairness of the machine learning model.
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Title: AI IN MEDICINE: ENABLING INTELLIGENT IMAGING, PROGNOSIS, AND MINIMALLY INVASIVE SURGERY
Creator: Getty, Neil
Date: 2022
Description: While an extremely rich research field, compared to other applications of AI such as natural language processing (NLP) and image processing...
Show moreWhile an extremely rich research field, compared to other applications of AI such as natural language processing (NLP) and image processing/generation, AI in medicine has been much slower to be applied in real-world clinical settings. Often the stakes of failure are more dire, the access of private and proprietary data more costly, and the burden of proof required by expert clinicians is much higher. Beyond these barriers, the often typical data-driven approach towards validation is interrupted by a need for expertise to analyze results. Whereas the results of a trained Imagenet or machine translation model are easily verified by a computational researcher, analysis in medicine can be much more multi-disciplinary demanding. AI in medicine is motivated by a great demand for progress in health-care, but an even greater responsibility for high accuracy, model transparency, and expert validation.This thesis develops machine and deep learning techniques for medical image enhancement, patient outcome prognosis, and minimally invasive robotic surgery awareness and augmentation. Each of the works presented were undertaken in di- rect collaboration with medical domain experts, and the efforts could not have been completed without them. Pursuing medical image enhancement we worked with radiologists, neuroscientists and a neurosurgeon. In patient outcome prognosis we worked with clinical neuropsychologists and a cardiovascular surgeon. For robotic surgery we worked with surgical residents and a surgeon expert in minimally invasive surgery. Each of these collaborations guided priorities for problem and model design, analysis, and long-term objectives that ground this thesis as a concerted effort towards clinically actionable medical AI. The contributions of this thesis focus on three specific medical domains. (1) Deep learning for medical brain scans: developed processing pipelines and deep learn- ing models for image annotation, registration, segmentation and diagnosis in both traumatic brain injury (TBI) and brain tumor cohorts. A major focus of these works is on the efficacy of low-data methods, and techniques for validation of results without any ground truth annotations. (2) Outcome prognosis for TBI and risk prediction for Cardiovascular Disease (CVD): we developed feature extraction pipelines and models for TBI and CVD patient clinical outcome prognosis and risk assessment. We design risk prediction models for CVD patients using traditional Cox modeling, machine learning, and deep learning techniques. In this works we conduct exhaustive data and model ablation study, with a focus on feature saliency analysis, model transparency, and usage of multi-modal data. (3) AI for enhanced and automated robotic surgery: we developed computer vision and deep learning techniques for understanding and augmenting minimally invasive robotic surgery scenes. We’ve developed models to recognize surgical actions from vision and kinematic data. Beyond model and techniques, we also curated novel datasets and prediction benchmarks from simulated and real endoscopic surgeries. We show the potential for self-supervised techniques in surgery, as well as multi-input and multi-task models.
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Title: ROBUST AND EXPLAINABLE RESULTS UTILIZING NEW METHODS AND NON-LINEAR MODELS
Creator: Onallah, Amir
Date: 2022
Description: This research focuses on robustness and explainability of new methods, and nonlinear analysis compared to traditional methods and linear...
Show moreThis research focuses on robustness and explainability of new methods, and nonlinear analysis compared to traditional methods and linear analysis. Further, it demonstrates that making assumptions, reducing the data, or simplifying the problem results in negative effect on the outcomes. This study utilizes the U.S. Patent Inventor database and the Medical Innovation dataset. Initially, we employ time-series models to enhance the quality of the results for event history analysis (EHA), add insights, and infer meanings, explanations, and conclusions. Then, we introduce newer algorithms of machine learning and machine learning with a time-to-event element to offer more robust methods than previous papers and reach optimal solutions by removing assumptions or simplifications of the problem, combine all data that encompasses the maximum knowledge, and provide nonlinear analysis.
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Title: Sharpen Quality Investing: A PLS-based Approach
Creator: Jiao, Zixuan
Date: 2022
Description: I apply a disciplined dimension reduction technique called Partial Least Square (PLS) to construct a new quality factor by aggregating...
Show moreI apply a disciplined dimension reduction technique called Partial Least Square (PLS) to construct a new quality factor by aggregating information from 16 individual signals. It earns significant risk-adjusted returns and outperforms quality factors constructed by alternative techniques, namely, PCA, Fama-Macbeth regression, a combination of PCA and Fama-Mabeth regression and a Rank-based approach. I show that my quality factor performs even better during rough economic patches and thus appears to hedge periods of market distress. I further show adding our quality factor to an opportunity set consisting of the other classical factors increases the maximum Sharpe ratio.
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Title: Data-Driven Methods for Soft Robot Control and Turbulent Flow Models
Creator: Lopez, Esteban Fernando
Date: 2022
Description: The world today has seen an exponential increase in its usage of computers for communication and measurement. Thanks to recent technologies,...
Show moreThe world today has seen an exponential increase in its usage of computers for communication and measurement. Thanks to recent technologies, we are now able to collect more data than ever before. This has dawned a new age of data-driven methods which can describe systems and behaviors with increasing accuracy. Whereas before we relied on the expertise of a few professionals with domain-specific knowledge developed over years of rigorous study, we are now able to rely on collected data to reveal patterns, develop novel ideas, and offer solutions to the world’s engineering problems. No domain is safe. Within the engineering realm, data-driven methods have seen vast usage in the areas of control and system identification. In this thesis we explore two areas of data-driven methods, namely reinforcement learning and data-driven causality. Reinforcement learning is a method by which an agent learns to increase its selection of ideal actions and behaviors which result in an increasing reward. This method was applied to a soft-robotic concept called the JAMoEBA to solve various tasks of interest in the robotics community, specifically tunnel navigation, obstacle field navigation, and object manipulation. A validation study was conducted to show the complications that arise when applying reinforcement learning to such a complex system. Nevertheless, it was shown that reinforcement learning is capable of solving three key tasks (static tunnel navigation, obstacle field navigation, and object manipulation) using specific simulation and learning hyperparameters. Data-driven causality encompasses a range of metrics and methods which attempt to uncover causal relationships between variables in a system. Several information theoretic causal metrics were developed and applied to nine mode turbulent flow data set which represents the Moehlis model. It was shown that careful consideration into the method used was required to identify significant causal relationships. Causal relationships were shown to converge over several hundred realizations of the turbulent model. Furthermore, these results match the expected causal relationships given known information of self-sustaining processes in turbulence, validating the method’s ability to identify causal relationships in turbulence.
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Title: Intelligent Job Scheduling on High Performance Computing Systems
Creator: Fan, Yuping
Date: 2021
Description: Job scheduler is a crucial component in high-performance computing (HPC) systems. It sorts and allocates jobs according to site policies and...
Show moreJob scheduler is a crucial component in high-performance computing (HPC) systems. It sorts and allocates jobs according to site policies and resource availability. It plays an important role in the efficient use of system resources and users satisfaction. Existing HPC job schedulers typically leverage simple heuristics to schedule jobs. However, the rapid growth in system infrastructure and the introduction of diverse workloads pose serious challenges to the traditional heuristic approaches. First, the current approaches concentrate on CPU footprint and ignore the performance of other resources. Second, the scheduling policies are manually designed and only consider some isolated job information, such as job size and runtime estimate. Such a manual design process prevents the schedulers from making informative decisions by extracting the abundant environment information (i.e., system and queue information). Moreover, they can hardly adapt to workload changes, leading to degraded scheduling performance. These challenges call for a new job scheduling framework that can extract useful information from diverse workloads and the increasingly complicated system environment, and finally make well-informed scheduling decisions in real time.In this work, we propose an intelligent HPC job scheduling framework to address these emerging challenges. Our research takes advantage of advanced machine learning and optimization methods to extract useful workload- and system-specific information and to further educate the framework to make efficient scheduling decisions under various system configurations and diverse workloads. The framework contains four major efforts. First, we focus on providing more accurate job runtime estimations. Estimated job runtime is one of the most important factors affecting scheduling decisions. However, user provided runtime estimates are highly inaccurate and existing solutions are prone to underestimation which causes jobs to be killed. We leverage and enhance a machine learning method called Tobit model to improve the accuracy of job runtime estimates at the same time reduce underestimation rate. More importantly, using TRIP’s improved job runtime estimates boosts scheduling performance by up to 45%. Second, we conduct research on multi-resource scheduling. HPC systems are undergoing significant changes in recent years. New hardware devices, such as GPU and burst buffer, have been integrated into production HPC systems, which significantly expands the schedulable resources. Unfortunately, the current production schedulers allocate jobs solely based on CPU footprint, which severely hurts system performance. In our work, we propose a framework taking all scalable resources into consideration by transforming this problem into multi-objective optimization (MOO) problem and rapid solving it via genetic algorithm. Next, we leverage reinforcement learning (RL) to automatically learn efficient workload- and system-specific scheduling policies. Existing HPC schedulers either use generalized and simple heuristics or optimization methods that ignore workload and system characteristics. To overcome this issue, we design a new scheduling agent DRAS to automatically learn efficient scheduling policies. DRAS leverages the advance in deep reinforcement learning and incorporates the key features of HPC scheduling in the form of a hierarchical neural network structure. We develop a three-phase training process to help DRAS effectively learn the scheduling environment (i.e., the system and its workloads) and to rapidly converge to an optimal policy. Finally, we explore the problem of scheduling mixed workloads, i.e., rigid, malleable and on-demand workloads, on a single HPC system. Traditionally, rigid jobs are the main tenants of HPC systems. In recent years, malleable applications, i.e., jobs that can change sizes before and during execution, are emerging on HPC systems. In addition, dedicated clusters were the main platforms to run on-demand jobs, i.e., jobs needed to be completed in the shortest time possible. As the sizes of on-demand jobs are growing, HPC systems become more cost-efficient platforms for on-demand jobs. However, existing studies do not consider the problem of scheduling all three types of workloads. In our work, we propose six mechanisms, which combine checkpointing, shrink, expansion techniques, to schedule the mixed workloads on one HPC system.
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Title: Towards Trustworthy Multiagent and Machine Learning Systems
Creator: Xie, Shangyu
Date: 2022
Description: This dissertation aims to systematically research the "trustworthy" Multiagent and Machine Learning systems in the context of the Internet of...
Show moreThis dissertation aims to systematically research the "trustworthy" Multiagent and Machine Learning systems in the context of the Internet of Things (IoT) system, which mainly consists of two aspects: data privacy and robustness. Specifically, data privacy concerns about the protection of the data in one given system, i.e., the data identified to be sensitive or private cannot be disclosed directly to others; robustness refers to the ability of the system to defend/mitigate the potential attacks/threats, i.e., maintaining the stable and normal operation of one system.Starting from the smart grid, a representative multiagent system in the IoT, I demonstrate two works on improving data privacy and robustness in aspects of different applications, load balancing and energy trading, which integrates secure multiparty computation (SMC) protocols for normal computation to ensure data privacy. More significantly, the schemes can be readily extended to other applications in IoT, e.g., connected vehicles, mobile sensing systems.For the machine learning, I have studied two main areas, i.e., computer vision and natural language processing with the privacy and robustness correspondingly. I first present the comprehensive robustness evaluation study of the DNN-based video recognition systems with two novel proposed attacks in both test and training phase, i.e., adversarial and poisoning attacks. Besides, I also propose the adaptive defenses to fully evaluate such two attacks, which can thus further advance the robustness of system. I also propose the privacy evaluation for the language systems and show the practice to reveal and address the privacy risks in the language models. Finally, I demonstrate a private and efficient data computation framework with the cloud computing technology to provide more robust and private IoT systems.
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