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- All Subjects: Computer Science
- Genre: Masters Thesis
- Creators: Baral, Chitta
- Resource Type: Text
Description
T-cells are an integral component of the immune system, enabling the body to distinguish between pathogens and the self. The primary mechanism which enables this is their T-cell receptors (TCR) which bind to antigen epitopes foreign to the body. This detection mechanism allows the T-cell to determine when an immune response is necessary. The computational prediction of TCR-epitope binding is important to researchers for both medical applications and for furthering their understanding of the biological mechanisms that impact immunity. Models which have been developed for this purpose fail to account for the interrelationships between amino acids and demonstrate poor out-of-sample performance. Small changes to the amino acids in these protein sequences can drastically change their structure and function. In recent years, attention-based deep learning models have shown success in their ability to learn rich contextual representations of data. To capture the contextual biological relationships between the amino acids, a multi-head self-attention model was created to predict the binding affinity between given TCR and epitope sequences. By learning the structural nuances of the sequences, this model is able to improve upon existing model performance and grant insights into the underlying mechanisms which impact binding.
ContributorsCai, Michael Ray (Author) / Lee, Heewook (Thesis advisor) / Bang, Seojin (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2021
Description
Artificial Intelligence, as the hottest research topic nowadays, is mostly driven by data. There is no doubt that data is the king in the age of AI. However, natural high-quality data is precious and rare. In order to obtain enough and eligible data to support AI tasks, data processing is always required. To be even worse, the data preprocessing tasks are often dull and heavy, which require huge human labors to deal with. Statistics show 70% - 80% of the data scientists' time is spent on data integration process. Among various reasons, schema changes that commonly exist in the data warehouse are one significant obstacle that impedes the automation of the end-to-end data integration process. Traditional data integration applications rely on data processing operators such as join, union, aggregation and so on. Those operations are fragile and can be easily interrupted by schema changes. Whenever schema changes happen, the data integration applications will require human labors to solve the interruptions and downtime. The industries as well as the data scientists need a new mechanism to handle the schema changes in data integration tasks. This work proposes a new direction of data integration applications based on deep learning models. The data integration problem is defined in the scenario of integrating tabular-format data with natural schema changes, using the cell-based data abstraction. In addition, data augmentation and adversarial learning are investigated to boost the model robustness to schema changes. The experiments are tested on two real-world data integration scenarios, and the results demonstrate the effectiveness of the proposed approach.
ContributorsWang, Zijie (Author) / Zou, Jia (Thesis advisor) / Baral, Chitta (Committee member) / Candan, K. Selcuk (Committee member) / Arizona State University (Publisher)
Created2021
Description
Code Generation is a task that has gained rapid progress in Natural Language Processing (NLP) research. This thesis focuses on the text-to-Structured Query Language (SQL) task, where the input is a question about a specific database and the output is the SQL that when executed will return the desired answer. The data creation process bottlenecks current text-to-SQL datasets. The technical knowledge required to understand and create SQL makes crowd-sourcing a dataset expensive and time-consuming. Thus, existing datasets do not provide a robust enough training set for state-of-the-art semantic parsing models. This thesis outlines my technique for generating a text-to-SQL dataset using GPT3 and prompt engineering techniques. My approach entails providing the Generative Pretrained Transformer 3 model (GPT-3) with particular instructions to build a rigorous text-to-SQL dataset. In this paper, I show that the created pairs have excellent quality and diversity, and when utilized as training data, they can enhance the accuracy of SQL generation models. I expect that my method will be of interest to academics in the disciplines of NLP because it can considerably reduce the time, effort, and cost necessary to produce large, high-quality text-to-SQL datasets. Furthermore, my approach can be extended to other tasks and domains to alleviate the burden of curating human-annotated data.
ContributorsKuznia, Kirby Charles (Author) / Baral, Chitta (Thesis advisor) / Blanco, Eduardo (Committee member) / Gopalan, Nakul (Committee member) / Arizona State University (Publisher)
Created2023
Description
Learning longer-horizon tasks is challenging with techniques such as reinforcement learning and behavior cloning. Previous approaches have split these long tasks into shorter tasks that are easier to learn by using statistical change point detection methods. However, classical changepoint detection methods function only with low-dimensional robot trajectory data and not with high-dimensional inputs such as vision. In this thesis, I have split a long horizon tasks, represented by trajectories into short-horizon sub-tasks with the supervision of language. These shorter horizon tasks can be learned using conventional behavior cloning approaches. I found comparisons between the techniques from the video moment retrieval problem and changepoint detection in robot trajectory data consisting of high-dimensional data. The proposed moment retrieval-based approach shows a more than 30% improvement in mean average precision (mAP) for identifying trajectory sub-tasks with language guidance compared to that without language. Several ablations are performed to understand the effects of domain randomization, sample complexity, views, and sim-to-real transfer of this method. The data ablation shows that just with a 100 labeled trajectories a 42.01 mAP can be achieved, demonstrating the sample efficiency of using such an approach. Further, behavior cloning models trained on the segmented trajectories outperform a single model trained on the whole trajectory by up to 20%.
ContributorsRaj, Divyanshu (Author) / Gopalan, Nakul (Thesis advisor) / Baral, Chitta (Committee member) / Senanayake, Ransalu (Committee member) / Arizona State University (Publisher)
Created2024
Description
The goal of fact checking is to determine if a given claim holds. A promising ap- proach for this task is to exploit reference information in the form of knowledge graphs (KGs), a structured and formal representation of knowledge with semantic descriptions of entities and relations. KGs are successfully used in multiple appli- cations, but the information stored in a KG is inevitably incomplete. In order to address the incompleteness problem, this thesis proposes a new method built on top of recent results in logical rule discovery in KGs called RuDik and a probabilistic extension of answer set programs called LPMLN.
This thesis presents the integration of RuDik which discovers logical rules over a given KG and LPMLN to do probabilistic inference to validate a fact. While automatically discovered rules over a KG are for human selection and revision, they can be turned into LPMLN programs with a minor modification. Leveraging the probabilistic inference in LPMLN, it is possible to (i) derive new information which is not explicitly stored in a KG with a probability associated with it, and (ii) provide supporting facts and rules for interpretable explanations for such decisions.
Also, this thesis presents experiments and results to show that this approach can label claims with high precision. The evaluation of the system also sheds light on the role played by the quality of the given rules and the quality of the KG.
This thesis presents the integration of RuDik which discovers logical rules over a given KG and LPMLN to do probabilistic inference to validate a fact. While automatically discovered rules over a KG are for human selection and revision, they can be turned into LPMLN programs with a minor modification. Leveraging the probabilistic inference in LPMLN, it is possible to (i) derive new information which is not explicitly stored in a KG with a probability associated with it, and (ii) provide supporting facts and rules for interpretable explanations for such decisions.
Also, this thesis presents experiments and results to show that this approach can label claims with high precision. The evaluation of the system also sheds light on the role played by the quality of the given rules and the quality of the KG.
ContributorsPradhan, Anish (Author) / Lee, Joohyung (Thesis advisor) / Baral, Chitta (Committee member) / Papotti, Paolo (Committee member) / Arizona State University (Publisher)
Created2018
Description
For the past three decades, the design of an effective strategy for generating poetry that matches that of a human’s creative capabilities and complexities has been an elusive goal in artificial intelligence (AI) and natural language generation (NLG) research, and among linguistic creativity researchers in particular. This thesis presents a novel approach to fixed verse poetry generation using neural word embeddings. During the course of generation, a two layered poetry classifier is developed. The first layer uses a lexicon based method to classify poems into types based on form and structure, and the second layer uses a supervised classification method to classify poems into subtypes based on content with an accuracy of 92%. The system then uses a two-layer neural network to generate poetry based on word similarities and word movements in a 50-dimensional vector space.
The verses generated by the system are evaluated using rhyme, rhythm, syllable counts and stress patterns. These computational features of language are considered for generating haikus, limericks and iambic pentameter verses. The generated poems are evaluated using a Turing test on both experts and non-experts. The user study finds that only 38% computer generated poems were correctly identified by nonexperts while 65% of the computer generated poems were correctly identified by experts. Although the system does not pass the Turing test, the results from the Turing test suggest an improvement of over 17% when compared to previous methods which use Turing tests to evaluate poetry generators.
The verses generated by the system are evaluated using rhyme, rhythm, syllable counts and stress patterns. These computational features of language are considered for generating haikus, limericks and iambic pentameter verses. The generated poems are evaluated using a Turing test on both experts and non-experts. The user study finds that only 38% computer generated poems were correctly identified by nonexperts while 65% of the computer generated poems were correctly identified by experts. Although the system does not pass the Turing test, the results from the Turing test suggest an improvement of over 17% when compared to previous methods which use Turing tests to evaluate poetry generators.
ContributorsMagge, Arjun (Author) / Syrotiuk, Violet R. (Thesis advisor) / Baral, Chitta (Committee member) / Hogue, Cynthia (Committee member) / Bazzi, Rida (Committee member) / Arizona State University (Publisher)
Created2016
Description
Modeling dynamic systems is an interesting problem in Knowledge Representation (KR) due to their usefulness in reasoning about real-world environments. In order to effectively do this, a number of different formalisms have been considered ranging from low-level languages, such as Answer Set Programming (ASP), to high-level action languages, such as C+ and BC. These languages show a lot of promise over many traditional approaches as they allow a developer to automate many tasks which require reasoning within dynamic environments in a succinct and elaboration tolerant manner. However, despite their strengths, they are still insufficient for modeling many systems, especially those of non-trivial scale or that require the ability to cope with exceptions which occur during execution, such as unexpected events or unintended consequences to actions which have been performed. In order to address these challenges, a theoretical framework is created which focuses on improving the feasibility of applying KR techniques to such problems. The framework is centered on the action language BC+, which integrates many of the strengths of existing KR formalisms, and provides the ability to perform efficient reasoning in an incremental fashion while handling exceptions which occur during execution. The result is a developer friendly formalism suitable for performing reasoning in an online environment. Finally, the newly enhanced Cplus2ASP 2 is introduced, which provides a number of improvements over the original version. These improvements include implementing BC+ among several additional languages, providing enhanced developer support, and exhibiting a significant performance increase over its predecessors and similar systems.
ContributorsBabb, Joseph (Author) / Lee, Joohyung (Thesis advisor) / Lee, Yann-Hang (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2014
Description
There have been extensive research in how news and twitter feeds can affect the outcome of a given stock. However, a majority of this research has studied the short term effects of sentiment with a given stock price. Within this research, I studied the long-term effects of a given stock price using fundamental analysis techniques. Within this research, I collected both sentiment data and fundamental data for Apple Inc., Microsoft Corp., and Peabody Energy Corp. Using a neural network algorithm, I found that sentiment does have an effect on the annual growth of these companies but the fundamentals are more relevant when determining overall growth. The stocks which show more consistent growth hold more importance on the previous year’s stock price but companies which have less consistency in their growth showed more reliance on the revenue growth and sentiment on the overall company and CEO. I discuss how I collected my research data and used a multi-layered perceptron to predict a threshold growth of a given stock. The threshold used for this particular research was 10%. I then showed the prediction of this threshold using my perceptron and afterwards, perform an f anova test on my choice of features. The results showed the fundamentals being the better predictor of stock information but fundamentals came in a close second in several cases, proving sentiment does hold an effect over long term growth.
ContributorsReeves, Tyler Joseph (Author) / Davulcu, Hasan (Thesis advisor) / Baral, Chitta (Committee member) / Cesta, John (Committee member) / Arizona State University (Publisher)
Created2016
Description
Due to vast resources brought by social media services, social data mining has
received increasing attention in recent years. The availability of sheer amounts of
user-generated data presents data scientists both opportunities and challenges. Opportunities are presented with additional data sources. The abundant link information
in social networks could provide another rich source in deriving implicit information
for social data mining. However, the vast majority of existing studies overwhelmingly
focus on positive links between users while negative links are also prevailing in real-
world social networks such as distrust relations in Epinions and foe links in Slashdot.
Though recent studies show that negative links have some added value over positive
links, it is dicult to directly employ them because of its distinct characteristics from
positive interactions. Another challenge is that label information is rather limited
in social media as the labeling process requires human attention and may be very
expensive. Hence, alternative criteria are needed to guide the learning process for
many tasks such as feature selection and sentiment analysis.
To address above-mentioned issues, I study two novel problems for signed social
networks mining, (1) unsupervised feature selection in signed social networks; and
(2) unsupervised sentiment analysis with signed social networks. To tackle the first problem, I propose a novel unsupervised feature selection framework SignedFS. In
particular, I model positive and negative links simultaneously for user preference
learning, and then embed the user preference learning into feature selection. To study the second problem, I incorporate explicit sentiment signals in textual terms and
implicit sentiment signals from signed social networks into a coherent model Signed-
Senti. Empirical experiments on real-world datasets corroborate the effectiveness of
these two frameworks on the tasks of feature selection and sentiment analysis.
received increasing attention in recent years. The availability of sheer amounts of
user-generated data presents data scientists both opportunities and challenges. Opportunities are presented with additional data sources. The abundant link information
in social networks could provide another rich source in deriving implicit information
for social data mining. However, the vast majority of existing studies overwhelmingly
focus on positive links between users while negative links are also prevailing in real-
world social networks such as distrust relations in Epinions and foe links in Slashdot.
Though recent studies show that negative links have some added value over positive
links, it is dicult to directly employ them because of its distinct characteristics from
positive interactions. Another challenge is that label information is rather limited
in social media as the labeling process requires human attention and may be very
expensive. Hence, alternative criteria are needed to guide the learning process for
many tasks such as feature selection and sentiment analysis.
To address above-mentioned issues, I study two novel problems for signed social
networks mining, (1) unsupervised feature selection in signed social networks; and
(2) unsupervised sentiment analysis with signed social networks. To tackle the first problem, I propose a novel unsupervised feature selection framework SignedFS. In
particular, I model positive and negative links simultaneously for user preference
learning, and then embed the user preference learning into feature selection. To study the second problem, I incorporate explicit sentiment signals in textual terms and
implicit sentiment signals from signed social networks into a coherent model Signed-
Senti. Empirical experiments on real-world datasets corroborate the effectiveness of
these two frameworks on the tasks of feature selection and sentiment analysis.
ContributorsCheng, Kewei (Author) / Liu, Huan (Thesis advisor) / Tong, Hanghang (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2017
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