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- Genre: Masters Thesis
- Creators: Davulcu, Hasan
Description
The overall contribution of the Minerva Initiative at ASU is to map social organizations in a multidimensional space that provides a measure of their radical or counter radical influence over the demographics of a nation. This tool serves as a simple content management system to store and track project resources like documents, images, videos and web links. It provides centralized and secure access to email conversations among project team members. Conversations are categorized into one of the seven pre-defined categories. Each category is associated with a certain set of keywords and we follow a frequency based approach for matching email conversations with the categories. The interface is hosted as a web application which can be accessed by the project team.
ContributorsNair, Apurva Aravindakshan (Author) / Davulcu, Hasan (Thesis advisor) / Sen, Arunabha (Committee member) / Dasgupta, Partha (Committee member) / Arizona State University (Publisher)
Created2012
Description
Continuous advancements in biomedical research have resulted in the production of vast amounts of scientific data and literature discussing them. The ultimate goal of computational biology is to translate these large amounts of data into actual knowledge of the complex biological processes and accurate life science models. The ability to rapidly and effectively survey the literature is necessary for the creation of large scale models of the relationships among biomedical entities as well as hypothesis generation to guide biomedical research. To reduce the effort and time spent in performing these activities, an intelligent search system is required. Even though many systems aid in navigating through this wide collection of documents, the vastness and depth of this information overload can be overwhelming. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also facilitate discovery of the unknown information implicitly conveyed in the texts. This thesis presents the different approaches used for large scale biomedical named entity recognition, and the challenges faced in each. It also proposes BioEve: an integrative framework to fuse a faceted search with information extraction to provide a search service that addresses the user's desire for "completeness" of the query results, not just the top-ranked ones. This information extraction system enables discovery of important semantic relationships between entities such as genes, diseases, drugs, and cell lines and events from biomedical text on MEDLINE, which is the largest publicly available database of the world's biomedical journal literature. It is an innovative search and discovery service that makes it easier to search
avigate and discover knowledge hidden in life sciences literature. To demonstrate the utility of this system, this thesis also details a prototype enterprise quality search and discovery service that helps researchers with a guided step-by-step query refinement, by suggesting concepts enriched in intermediate results, and thereby facilitating the "discover more as you search" paradigm.
avigate and discover knowledge hidden in life sciences literature. To demonstrate the utility of this system, this thesis also details a prototype enterprise quality search and discovery service that helps researchers with a guided step-by-step query refinement, by suggesting concepts enriched in intermediate results, and thereby facilitating the "discover more as you search" paradigm.
ContributorsKanwar, Pradeep (Author) / Davulcu, Hasan (Thesis advisor) / Dinu, Valentin (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2010
Description
Text search is a very useful way of retrieving document information from a particular website. The public generally use internet search engines over the local enterprise search engines, because the enterprise content is not cross linked and does not follow a page rank algorithm. On the other hand the enterprise search engine uses metadata information, which allows the user to specify the conditions that any retrieved document should meet. Therefore, using metadata information for searching will also be very useful. My thesis aims on developing an enterprise search engine using metadata information by providing advanced features like faceted navigation. The search engine data was extracted from various Indonesian web sources. Metadata information like person, organization, location, and sentiment analytic keyword entities should be tagged in each document to provide facet search capability. A shallow parsing technique like named entity recognizer is used for this purpose. There are more than 1500 entities that have been tagged in this process. These documents have been successfully converted into XML format and are indexed with "Apache Solr". It is an open source enterprise search engine with full text search and faceted search capabilities. The entities will be helpful for users to specify conditions and search faster through the large collection of documents. The user is assured results by clicking on a metadata condition. Since the sentiment analytic keywords are tagged with positive and negative values, social scientists can use these results to check for overlapping or conflicting organizations and ideologies. In addition, this tool is the first of its kind for the Indonesian language. The results are fetched much faster and with better accuracy.
ContributorsSanaka, Srinivasa Raviteja (Author) / Davulcu, Hasan (Thesis advisor) / Sen, Arunabha (Committee member) / Taylor, Thomas (Committee member) / Arizona State University (Publisher)
Created2010
Description
In recent years, there are increasing numbers of applications that use multi-variate time series data where multiple uni-variate time series coexist. However, there is a lack of systematic of multi-variate time series. This thesis focuses on (a) defining a simplified inter-related multi-variate time series (IMTS) model and (b) developing robust multi-variate temporal (RMT) feature extraction algorithm that can be used for locating, filtering, and describing salient features in multi-variate time series data sets. The proposed RMT feature can also be used for supporting multiple analysis tasks, such as visualization, segmentation, and searching / retrieving based on multi-variate time series similarities. Experiments confirm that the proposed feature extraction algorithm is highly efficient and effective in identifying robust multi-scale temporal features of multi-variate time series.
ContributorsWang, Xiaolan (Author) / Candan, Kasim Selcuk (Thesis advisor) / Sapino, Maria Luisa (Committee member) / Fainekos, Georgios (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Learning from high dimensional biomedical data attracts lots of attention recently. High dimensional biomedical data often suffer from the curse of dimensionality and have imbalanced class distributions. Both of these features of biomedical data, high dimensionality and imbalanced class distributions, are challenging for traditional machine learning methods and may affect the model performance. In this thesis, I focus on developing learning methods for the high-dimensional imbalanced biomedical data. In the first part, a sparse canonical correlation analysis (CCA) method is presented. The penalty terms is used to control the sparsity of the projection matrices of CCA. The sparse CCA method is then applied to find patterns among biomedical data sets and labels, or to find patterns among different data sources. In the second part, I discuss several learning problems for imbalanced biomedical data. Note that traditional learning systems are often biased when the biomedical data are imbalanced. Therefore, traditional evaluations such as accuracy may be inappropriate for such cases. I then discuss several alternative evaluation criteria to evaluate the learning performance. For imbalanced binary classification problems, I use the undersampling based classifiers ensemble (UEM) strategy to obtain accurate models for both classes of samples. A small sphere and large margin (SSLM) approach is also presented to detect rare abnormal samples from a large number of subjects. In addition, I apply multiple feature selection and clustering methods to deal with high-dimensional data and data with highly correlated features. Experiments on high-dimensional imbalanced biomedical data are presented which illustrate the effectiveness and efficiency of my methods.
ContributorsYang, Tao (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Social media has become a primary means of communication and a prominent source of information about day-to-day happenings in the contemporary world. The rise in the popularity of social media platforms in recent decades has empowered people with an unprecedented level of connectivity. Despite the benefits social media offers, it also comes with disadvantages. A significant downside to staying connected via social media is the susceptibility to falsified information or Fake News. Easy accessibility to social media and lack of truth verification tools favored the miscreants on online platforms to spread false propaganda at scale, ensuing chaos. The spread of misinformation on these platforms ultimately leads to mistrust and social unrest. Consequently, there is a need to counter the spread of misinformation which could otherwise have a detrimental impact on society. A notable example of such a case is the 2019 Covid pandemic misinformation spread, where coordinated misinformation campaigns misled the public on vaccination and health safety. The advancements in Natural Language Processing gave rise to sophisticated language generation models that can generate realistic-looking texts. Although the current Fake News generation process is manual, it is just a matter of time before this process gets automated at scale and generates Neural Fake News using language generation models like the Bidirectional Encoder Representations from Transformers (BERT) and the third generation Generative Pre-trained Transformer (GPT-3). Moreover, given that the current state of fact verification is manual, it calls for an urgent need to develop reliable automated detection tools to counter Neural Fake News generated at scale. Existing tools demonstrate state-of-the-art performance in detecting Neural Fake News but exhibit a black box behavior. Incorporating explainability into the Neural Fake News classification task will build trust and acceptance amongst different communities and decision-makers. Therefore, the current study proposes a new set of interpretable discriminatory features. These features capture statistical and stylistic idiosyncrasies, achieving an accuracy of 82% on Neural Fake News classification. Furthermore, this research investigates essential dependency relations contributing to the classification process. Lastly, the study concludes by providing directions for future research in building explainable tools for Neural Fake News detection.
ContributorsKarumuri, Ravi Teja (Author) / Liu, Huan (Thesis advisor) / Corman, Steven (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2022
Description
Bitcoin (BTC) shares many characteristics with traditional stocks, but it is much more volatile since the cryptocurrency market is unregulated. The high volatility makes BTC a very high risk-high reward investment and predictive analysis can be very useful to obtain good returns and minimize risk. Taking Cocco et al. [1] as the primary reference, this thesis tries to reproduce their findings by building two BTC price forecasting models, Long Short-Term Memory (LSTM) and Bayesian Neural Network (BNN), and finding that the Mean Absolute Percentage Error (MAPE) is lower for the initial BNN model in comparison to the initial LSTM model. In addition to forecasting the value of BTC, a metric called trend% is developed to gauge the models’ ability to capture the trend of how the price varies from one timestep to the next and used to compare the trend prediction performance. It is found that both initial models make random predictions for the trend. Improvements like removing the stochastic component from the data and forecasting returns as opposed to price values show that both models show comparable performance in terms of both MAPE and trend%. The thesis concludes by discussing the future work that can be done to potentially improve the above models. One of the possibilities mentioned is to use on-chain data from the BTC blockchain coupled with the real-world knowledge of BTC exchanges and feed this as input features to the models.
ContributorsMittal, Shivansh (Author) / Boscovic, Dragan (Thesis advisor) / Davulcu, Hasan (Committee member) / Candan, Kasim (Committee member) / Arizona State University (Publisher)
Created2022
Description
In some scenarios, true temporal ordering is required to identify the actions occurring in a video. Recently a new synthetic dataset named CATER, was introduced containing 3D objects like sphere, cone, cylinder etc. which undergo simple movements such as slide, pick & place etc. The task defined in the dataset is to identify compositional actions with temporal ordering. In this thesis, a rule-based system and a window-based technique are proposed to identify individual actions (atomic) and multiple actions with temporal ordering (composite) on the CATER dataset. The rule-based system proposed here is a heuristic algorithm that evaluates the magnitude and direction of object movement across frames to determine the atomic action temporal windows and uses these windows to predict the composite actions in the videos. The performance of the rule-based system is validated using the frame-level object coordinates provided in the dataset and it outperforms the performance of the baseline models on the CATER dataset. A window-based training technique is proposed for identifying composite actions in the videos. A pre-trained deep neural network (I3D model) is used as a base network for action recognition. During inference, non-overlapping windows are passed through the I3D network to obtain the atomic action predictions and the predictions are passed through a rule-based system to determine the composite actions. The approach outperforms the state-of-the-art composite action recognition models by 13.37% (mAP 66.47% vs. mAP 53.1%).
ContributorsMaskara, Vivek Kumar (Author) / Venkateswara, Hemanth (Thesis advisor) / McDaniel, Troy (Thesis advisor) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2022
Description
Large Language Models (LLMs) have displayed impressive capabilities in handling tasks that require few demonstration examples, making them effective few-shot learn- ers. Despite their potential, LLMs face challenges when it comes to addressing com- plex real-world tasks that involve multiple modalities or reasoning steps. For example, predicting cancer patients’ survival period based on clinical data, cell slides, and ge- nomics poses significant logistical complexities. Although several approaches have been proposed to tackle these challenges, they often fall short in achieving promising performance due to their inability to consider all modalities simultaneously or account for missing modalities, variations in modalities, and the integration of multi-modal data, ultimately compromising their effectiveness.This thesis proposes a novel approach for multi-modal tumor survival prediction to address these limitations. Taking inspiration from recent advancements in LLMs, particularly Mixture of Experts (MoE)-based models, a graph-guided MoE framework is introduced. This framework utilizes a graph structure to manage the predictions effectively and combines multiple models to enhance predictive power. Rather than training a single foundation model for end-to-end survival prediction, the approach leverages a MOE-guided ensemble to manage model callings as tools automatically. By leveraging the strengths of existing models and guiding them through a MOE framework, the aim is to achieve better performance and more accurate predictions in complex real-world tasks. Experiments and analysis on the TCGA-LUAD dataset show improved performance over the individual modal and vanilla ensemble models.
ContributorsMathavan, Hirthik (Author) / Liu, Huan (Thesis advisor) / Davulcu, Hasan (Committee member) / Choi, YooJung (Committee member) / Arizona State University (Publisher)
Created2024
Description
Animal pose estimation (APE) is utilized in preclinical research settings for various neurological disorders such as Parkinson's disease (PD), Huntington's disease (HD) and multiple sclerosis. The technique includes real-time scoring of impairment in the animals during testing or video recording. This is a time-consuming operation prone to errors due to visual fatigue. To overcome these shortcomings, APE automation by deep learning has been studied. The field of APE has gone through significant development backed by improvements in deep learning techniques. These developments have improved 2D and 3D pose estimation, 3D mesh reconstruction and behavior prediction capabilities. As a result, there are numerous sophisticated tools and datasets available today. Despite these developments, APE still lags behind human observer scoring with respect to accuracy and flexibility under complex scenarios. In this project, two critical challenges are being addressed within the context of neurological research focusing on PD. The first challenge is about the lack of comprehensive diverse datasets necessary for accurate training as well as for fine-tuning deep learning models. This is compounded by the inherent difficulty in working with uncooperative rodent subjects, whose unpredictable behaviors often impede reliable data collection. The second challenge focuses on reduction in variation of scores that result from being scored by different evaluators. This will also involve tackling bias and reducing human error for the purpose of reliable and accurate assessments. In order to address these issues, systematic data collection and deep learning in APE have been utilized to automate manual scoring procedures. This project will contribute to neurological research, particularly in understanding and treating disorders like PD. The goal is to improve methods used in assessing rodent behavior which could aid in developing effective therapeutics. The successful implementation of an automated scoring mechanism could set a new standard in neurological research, offering insights and methodologies that are more accurate and reliable.
ContributorsJanapareddi, Ajay Kumar (Author) / Davulcu, Hasan (Thesis advisor) / Poste, George (Thesis advisor) / Kelley, Christy (Committee member) / Arizona State University (Publisher)
Created2024