The ability to automatically detect and repair vulnerabilities in code before deployment has become the subject of increasing attention. Some approaches to this problem rely on machine learning techniques, however the lack of datasets–code samples labeled as containing a vulnerability or not–presents a barrier to performance. We design and implement a deep neural network based on the recently developed Grammar Variational Autoencoder (VAE) architecture to generate an arbitrary number of unique C functions labeled in the aforementioned manner. We make several improvements on the original Grammar VAE: we guarantee that every vector in the neural network’s latent space decodes to a syntactically valid C function; we extend the Grammar VAE into a context-sensitive environment; and we implement a semantic repair algorithm that transforms syntactically valid C functions into fully semantically valid C functions that compile and execute. Users can control the semantic qualities of output functions with our constraint system. Our constraints allow users to modify the return type, change control flow structures, inject vulnerabilities into generated code, and more. We demonstrate the advantages of our model over other program synthesis models targeting similar applications. We also explore alternative applications for our model, including code plagiarism detection and compiler fuzzing, testing, and optimization.

Indiana University-Purdue University Indianapolis (IUPUI) / This study mainly focuses on applying visualization techniques on human brain data for data exploration, quality control, and hypothesis discovery. It mainly consists of two parts: multi-modal data visualization and interactive machine learning. For multi-modal data visualization, a major challenge is how to integrate structural, functional and connectivity data to form a comprehensive visual context. We develop a new integrated visualization solution for brain imaging data by combining scientific and information visualization techniques within the context of the same anatomic structure. For interactive machine learning, we propose a new visual analytics approach to interactive machine learning. In this approach, multi-dimensional data visualization techniques are employed to facilitate user interactions with the machine learning process. This allows dynamic user feedback in different forms, such as data selection, data labeling, and data correction, to enhance the efficiency of model building.

Indiana University-Purdue University Indianapolis (IUPUI) / Meningioma represent more than one-third of all primary central nervous system (CNS) tumors, and it can be classified into three grades according to WHO (World Health Organization) in terms of clinical aggressiveness and risk of recurrence. A key component of meningioma grades is the mitotic count, which is defined as quantifying the number of cells in the process of dividing (i.e., undergoing mitosis) at a specific point in time. Currently, mitosis counting is done manually by a pathologist looking at 10 consecutive high-power fields (HPF) on a glass slide under a microscope, which is an extremely laborious and time-consuming process. The goal of this thesis is to investigate the use of computerized methods to automate the detection of mitotic nuclei with limited labeled data. We built computational methods to detect and quantify the histological features of mitotic cells on a whole slides image which mimic the exact process of pathologist workflow. Since we do not have enough training data from meningioma slide, we learned the mitotic cell features through public available breast cancer datasets, and predicted on meingioma slide for accuracy. We use either handcrafted features that capture certain morphological, statistical, or textural attributes of mitoses or features learned with convolutional neural networks (CNN). Hand crafted features are inspired by the domain knowledge, while the data-driven VGG16 models tend to be domain agnostic and attempt to learn additional feature bases that cannot be represented through any of the handcrafted features. Our work on detection of mitotic cells shows 100% recall , 9% precision and 0.17 F1 score. The detection using VGG16 performs with 71% recall, 73% precision, and 0.77 F1 score. Finally, this research of automated image analysis could drastically increase diagnostic efficiency and reduce inter-observer variability and errors in pathology diagnosis, which would allow fewer pathologists to serve more patients while maintaining diagnostic accuracy and precision. And all these methodologies will increasingly transform practice of pathology, allowing it to mature toward a quantitative science.

For input data of homogenous type, the standard form of convolutional neural network is normally constructed with universally applied filters to identify global patterns. However, for certain datasets, there are identifiable trends and patterns within subgroups of input data. This research proposes a convolutional neural network that deliberately partitions input data into groups to be processed with unique sets of convolutional layers, thus identifying the underlying features of individual data groups. Training and testing data are built from historical prices of stock market and preprocessed so that the generated datasets are suitable for both standard and the proposed convolutional neural network. The author of this research also developed a software framework that can construct neural networks to perform necessary testing. The calculation logic was implemented using parallel programming and executed on a Nvidia graphic processing unit, thus allowing tests to be executed without expensive hardware. Tests were executed for 134 sets of datasets to benchmark the performance between standard and the proposed convolutional neural network. Test results show that the partitioned convolution method is capable of performance that rivals its standard counterpart. Further analysis indicates that more sophisticated method of building datasets, larger sets of training data, or more training epochs can further improve the performance of the partitioned neural network. For suitable datasets, the proposed method could be a viable replacement or supplement to the standard convolutional neural network structure. / Thesis / Master of Applied Science (MASc) / A convolutional neural network is a machine learning tool that allows complex patterns in datasets to be identified and modelled. For datasets with input that consists of the same type of data, a convolutional neural network is often architected to identify global patterns. This research explores the viability of partitioning input data into groups and processing them with separate convolutional layers so unique patterns associated with individual subgroups of input data can be identified. The author of this research built suitable test datasets and developed a (parallel computation enabled) framework that can construct both standard and proposed convolutional neural networks. The test results show that the proposed structure is capable of performance that matches its standard counterpart. Further analysis indicates that there are potential methods to further improve the performance of partitioned convolution, making it a viable replacement or supplement to standard convolution.

Nowadays, machine learning methods are used in many applications and deployed in manyelectronic devices to solve problems and predict future states. One of the challenges mostbig cities confront is traffic jams since the roads are crammed with more and more vehicles, which will easily cause traffic congestion. Traffic jams are not environment-friendly,but scientific planning can minimize their effect. Traffic prediction is one of the most interesting subjects for Intelligent transportation systems due to its ability to prevent trafficjams with the knowledge of the predictions. Traffic prediction is a very challenging taskfor researchers to find or implement a model to perform accurately in different scenarios.Accurate traffic forecasting has become an essential mission for intelligent transportationsystems, which improve transportation efficiency, safety, and sustainability using moderntechnology and data analysis. Capturing both temporal and spatial dependencies is one ofthe most essential key in traffic prediction. Combining two or several models is one way tocapture both dependencies. A temporal graph convolutional network (T-GCN) is a graphneural network model, a combination of a graph convolutional network and a gated recurrent unit (GRU). In T-GCN, a graph convolutional network (GCN) is used to capture spatialwhile recurrent gated units to capture temporal dependencies. One of the main issues ofT-GCN is long-term prediction failure, where the model’s accuracy decreases when the prediction length increases. In this paper, we propose a Decomposed Temporal Self-AttentionMulti-layer Graph Convolutional network (DTSA-3GCN) to enhance overall traffic prediction in different horizons based on Singular Value Decomposition (SVD), Self-Attention(SA), and a Temporal Multi-layer Graph Convolutional Network. The experiment resultdemonstrates that DTSA-3GCN outperforms the state-of-the-art models such as T-GCN,A3T-GCN, and STGODE.

Artificial Neural networks have found many applications in various fields such as function approximation, time-series prediction, and adaptive control. The performance of a neural network depends on many factors, including the network structure, the selection of activation functions, the learning rate of the training algorithm, and initial synaptic weight values, etc. Genetic algorithms are inspired by Charles Darwin’s theory of natural selection (“survival of the fittest”). They are heuristic search techniques that are based on aspects of natural evolution, such as inheritance, mutation, selection, and crossover. This research utilizes a genetic algorithm to optimize multi-layer feedforward neural network performance and structure. The goal is to minimize both the function of output errors and the number of connections of network. The algorithm is modeled in C++ and tested on several different data sets. Computer simulation results show that the proposed algorithm can successfully determine the appropriate network size for optimal performance. This research also includes studies of the effects of population size, crossover type, probability of bit mutation, and the error scaling factor.

Tracab’s optical tracking system allows to track the 2-dimensional trajectories of players and ball during a football game. Using this data it is possible to train machine learning models to identify events that happen during the match. In this thesis, we explore the detection of corners, free kicks, and throw-in events by means of neural networks. Training a model to solve this task is not easy; the neural network needs to model the spatio-temporal interactions between different agents moving in a 2-dimensional space. We decided to address this problem using graph neural networks in combination with recurrent neural networks, which allow us to model respectively the spatial and temporal components of the data. Tracking the position of the ball is difficult, which makes the dataset noisy. In this thesis, we mainly work with a version of the dataset where the position of the ball has been manually corrected. However, to study how the noisy position of the ball affects the results we also train the models on the original data. The results show that detecting the corner and the throw-in is much easier than detecting the free kick. Moreover, the noisy position of the ball affects significantly the performance of the model. We conclude that to train the model on the original data it is necessary to use a much larger training set. Since the amount of training data for these events is limited, we also train the model on the more generic ball-dead-to-alive event, for which much more data is available, and we observe that by increasing the amount of training data the results can improve significantly. In this report, we also provide an in-depth discussion about all the challenges faced during the project and how different hyperparameters and design choices can affect the results. / Tracabs optiska spårningssystem gör det möjligt att spåra de 2-dimensionella banorna för spelare och boll under en fotbollsmatch. Med hjälp av dessa data är det möjligt att träna maskininlärningsmodeller för att identifiera händelser som inträffar under matchen. I denna avhandling utforskar vi upptäckten av hörnor, frisparkar och inkastningshändelser med hjälp av neurala nätverk. Att träna en modell för att lösa denna uppgift är inte lätt; det neurala nätverket behöver modellera de rums-temporala interaktionerna mellan olika agenter som rör sig i ett 2-dimensionellt rum. Vi bestämde oss för att ta itu med detta problem med hjälp av grafiska neurala nätverk i kombination med återkommande neurala nätverk, vilket gör att vi kan modellera de rumsliga respektive temporala komponenterna i datan. Det är svårt att spåra bollens position, vilket gör datauppsättningen bullrig. I detta examensarbete arbetar vi främst med en version av datamängden där bollens position har korrigerats manuellt. Men för att studera hur bollens bullriga position påverkar resultaten tränar vi också modellerna på originaldata. Resultaten visar att det är mycket lättare att upptäcka hörna och inkastet än att upptäcka frisparken. Dessutom påverkar bollens bullriga position avsevärt modellens prestanda. Vi drar slutsatsen att för att träna modellen på originaldata är det nödvändigt att använda en mycket större träningsuppsättning. Eftersom mängden träningsdata för dessa evenemang är begränsad, tränar vi också modellen på den mer generiska bollen död-till-levande-händelsen, för vilken mycket mer data finns tillgänglig, och vi observerar att genom att öka mängden träningsdata resultaten kan förbättras avsevärt. I denna rapport ger vi också en fördjupad diskussion om alla utmaningar som ställs inför under projektet och hur olika hyperparametrar och designval kan påverka resultaten.

Probabilistic behavior in perceiving the environment and take critical decisions have an inevitable role in human life. A decision is concerned with a choice among the available alternatives and is always subject to unknown elements concerning the future. The lack of complete data, insufficient scientific, behavioral, and industry development and of course defects in measurement methods, affect the reliability of an action’s outcome. Thus, having a proper estimation of this reliability or uncertainty could be very advantageous particularly when an individual or generally a subject is faced with a high risk. With the fact that there are always uncertainty elements whose values are unknown and these enter into a processes through multiple sources, it has been a primary challenge to design an efficient representation of confidence objectively. With the aim of addressing this problem, a variety of researches have been conducted to introduce frameworks in metrology of uncertainty quantification that are comprehensive enough and have transferability into different areas. Moreover, it’s also a challenging task to define a proper index that reflects more aspects of the problem and measurement process. With significant advances in Artificial Intelligence in the past decade, one of the key elements, in order to ease human life by giving more control to machines, is to heed the uncertainty estimation for a prediction. With a focus on measurement aspects, this thesis attends to demonstrate how a different measurement index affects the quality of evaluated predictive uncertainty of neural networks. Finally, we propose a novel index that shows uncertainty values with the same or higher quality than existing methods which emphasizes the benefits of having a proper measurement index in managing the risk of the outcome from a classification model.

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