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As we migrate into an era of personalized medicine, understanding how bio-molecules interact with one another to form cellular systems is one of the key focus areas of systems biology. Several challenges such as the dynamic nature of cellular systems, uncertainty due to environmental influences, and the heterogeneity between individual

As we migrate into an era of personalized medicine, understanding how bio-molecules interact with one another to form cellular systems is one of the key focus areas of systems biology. Several challenges such as the dynamic nature of cellular systems, uncertainty due to environmental influences, and the heterogeneity between individual patients render this a difficult task. In the last decade, several algorithms have been proposed to elucidate cellular systems from data, resulting in numerous data-driven hypotheses. However, due to the large number of variables involved in the process, many of which are unknown or not measurable, such computational approaches often lead to a high proportion of false positives. This renders interpretation of the data-driven hypotheses extremely difficult. Consequently, a dismal proportion of these hypotheses are subject to further experimental validation, eventually limiting their potential to augment existing biological knowledge. This dissertation develops a framework of computational methods for the analysis of such data-driven hypotheses leveraging existing biological knowledge. Specifically, I show how biological knowledge can be mapped onto these hypotheses and subsequently augmented through novel hypotheses. Biological hypotheses are learnt in three levels of abstraction -- individual interactions, functional modules and relationships between pathways, corresponding to three complementary aspects of biological systems. The computational methods developed in this dissertation are applied to high throughput cancer data, resulting in novel hypotheses with potentially significant biological impact.
ContributorsRamesh, Archana (Author) / Kim, Seungchan (Thesis advisor) / Langley, Patrick W (Committee member) / Baral, Chitta (Committee member) / Kiefer, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Emotion recognition in conversation has applications within numerous domains such as affective computing and medicine. Recent methods for emotion recognition jointly utilize conversational data over several modalities including audio, video, and text. However, state-of-the-art frameworks for this task do not focus on the feature extraction and feature fusion steps of

Emotion recognition in conversation has applications within numerous domains such as affective computing and medicine. Recent methods for emotion recognition jointly utilize conversational data over several modalities including audio, video, and text. However, state-of-the-art frameworks for this task do not focus on the feature extraction and feature fusion steps of this process. This thesis aims to improve the state-of-the-art method by incorporating two components to better accomplish these steps. By doing so, we are able to produce improved representations for the text modality and better model the relationships between all modalities. This paper proposes two methods which focus on these concepts and provide improved accuracy over the state-of-the-art framework for multimodal emotion recognition in dialogue.
ContributorsRawal, Siddharth (Author) / Baral, Chitta (Thesis director) / Shah, Shrikant (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
Medical records are increasingly being recorded in the form of electronic health records (EHRs), with a significant amount of patient data recorded as unstructured natural language text. Consequently, being able to extract and utilize clinical data present within these records is an important step in furthering clinical care. One important

Medical records are increasingly being recorded in the form of electronic health records (EHRs), with a significant amount of patient data recorded as unstructured natural language text. Consequently, being able to extract and utilize clinical data present within these records is an important step in furthering clinical care. One important aspect within these records is the presence of prescription information. Existing techniques for extracting prescription information — which includes medication names, dosages, frequencies, reasons for taking, and mode of administration — from unstructured text have focused on the application of rule- and classifier-based methods. While state-of-the-art systems can be effective in extracting many types of information, they require significant effort to develop hand-crafted rules and conduct effective feature engineering. This paper presents the use of a bidirectional LSTM with CRF tagging model initialized with precomputed word embeddings for extracting prescription information from sentences without requiring significant feature engineering. The experimental results, run on the i2b2 2009 dataset, achieve an F1 macro measure of 0.8562, and scores above 0.9449 on four of the six categories, indicating significant potential for this model.
ContributorsRawal, Samarth Chetan (Author) / Baral, Chitta (Thesis director) / Anwar, Saadat (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
In this project, the use of deep neural networks for the process of selecting actions to execute within an environment to achieve a goal is explored. Scenarios like this are common in crafting based games such as Terraria or Minecraft. Goals in these environments have recursive sub-goal dependencies which form

In this project, the use of deep neural networks for the process of selecting actions to execute within an environment to achieve a goal is explored. Scenarios like this are common in crafting based games such as Terraria or Minecraft. Goals in these environments have recursive sub-goal dependencies which form a dependency tree. An agent operating within these environments have access to low amounts of data about the environment before interacting with it, so it is crucial that this agent is able to effectively utilize a tree of dependencies and its environmental surroundings to make judgements about which sub-goals are most efficient to pursue at any point in time. A successful agent aims to minimizes cost when completing a given goal. A deep neural network in combination with Q-learning techniques was employed to act as the agent in this environment. This agent consistently performed better than agents using alternate models (models that used dependency tree heuristics or human-like approaches to make sub-goal oriented choices), with an average performance advantage of 33.86% (with a standard deviation of 14.69%) over the best alternate agent. This shows that machine learning techniques can be consistently employed to make goal-oriented choices within an environment with recursive sub-goal dependencies and low amounts of pre-known information.
ContributorsKoleber, Derek (Author) / Acuna, Ruben (Thesis director) / Bansal, Ajay (Committee member) / W.P. Carey School of Business (Contributor) / Software Engineering (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
One persisting problem in Massive Open Online Courses (MOOCs) is the issue of student dropout from these courses. The prediction of student dropout from MOOC courses can identify the factors responsible for such an event and it can further initiate intervention before such an event to increase student success in

One persisting problem in Massive Open Online Courses (MOOCs) is the issue of student dropout from these courses. The prediction of student dropout from MOOC courses can identify the factors responsible for such an event and it can further initiate intervention before such an event to increase student success in MOOC. There are different approaches and various features available for the prediction of student’s dropout in MOOC courses.In this research, the data derived from the self-paced math course ‘College Algebra and Problem Solving’ offered on the MOOC platform Open edX offered by Arizona State University (ASU) from 2016 to 2020 was considered. This research aims to predict the dropout of students from a MOOC course given a set of features engineered from the learning of students in a day. Machine Learning (ML) model used is Random Forest (RF) and this model is evaluated using the validation metrics like accuracy, precision, recall, F1-score, Area Under the Curve (AUC), Receiver Operating Characteristic (ROC) curve. The average rate of student learning progress was found to have more impact than other features. The model developed can predict the dropout or continuation of students on any given day in the MOOC course with an accuracy of 87.5%, AUC of 94.5%, precision of 88%, recall of 87.5%, and F1-score of 87.5% respectively. The contributing features and interactions were explained using Shapely values for the prediction of the model. The features engineered in this research are predictive of student dropout and could be used for similar courses to predict student dropout from the course. This model can also help in making interventions at a critical time to help students succeed in this MOOC course.
ContributorsDominic Ravichandran, Sheran Dass (Author) / Gary, Kevin (Thesis advisor) / Bansal, Ajay (Committee member) / Cunningham, James (Committee member) / Sannier, Adrian (Committee member) / Arizona State University (Publisher)
Created2021
Description

In this thesis, several different methods for detecting and removing satellite streaks from astronomic images were evaluated and compared with a new machine learning based approach. Simulated data was generated with a variety of conditions, and the performance of each method was evaluated both quantitatively, using Mean Absolute Error (MAE)

In this thesis, several different methods for detecting and removing satellite streaks from astronomic images were evaluated and compared with a new machine learning based approach. Simulated data was generated with a variety of conditions, and the performance of each method was evaluated both quantitatively, using Mean Absolute Error (MAE) against a ground truth detection mask and processing throughput of the method, as well as qualitatively, examining the situations in which each model performs well and poorly. Detection methods from existing systems Pyradon and ASTRiDE were implemented and tested. A machine learning (ML) image segmentation model was trained on simulated data and used to detect streaks in test data. The ML model performed favorably relative to the traditional methods tested, and demonstrated superior robustness in general. However, the model also exhibited some unpredictable behavior in certain scenarios which should be considered. This demonstrated that machine learning is a viable tool for the detection of satellite streaks in astronomic images, however special care must be taken to prevent and to minimize the effects of unpredictable behavior in such models.

ContributorsJeffries, Charles (Author) / Acuna, Ruben (Thesis director) / Martin, Thomas (Committee member) / Bansal, Ajay (Committee member) / Barrett, The Honors College (Contributor) / Software Engineering (Contributor)
Created2023-05
Description

The aim of this project is to understand the basic algorithmic components of the transformer deep learning architecture. At a high level, a transformer is a machine learning model based off of a recurrent neural network that adopts a self-attention mechanism, which can weigh significant parts of sequential input data

The aim of this project is to understand the basic algorithmic components of the transformer deep learning architecture. At a high level, a transformer is a machine learning model based off of a recurrent neural network that adopts a self-attention mechanism, which can weigh significant parts of sequential input data which is very useful for solving problems in natural language processing and computer vision. There are other approaches to solving these problems which have been implemented in the past (i.e., convolutional neural networks and recurrent neural networks), but these architectures introduce the issue of the vanishing gradient problem when an input becomes too long (which essentially means the network loses its memory and halts learning) and have a slow training time in general. The transformer architecture’s features enable a much better “memory” and a faster training time, which makes it a more optimal architecture in solving problems. Most of this project will be spent producing a survey that captures the current state of research on the transformer, and any background material to understand it. First, I will do a keyword search of the most well cited and up-to-date peer reviewed publications on transformers to understand them conceptually. Next, I will investigate any necessary programming frameworks that will be required to implement the architecture. I will use this to implement a simplified version of the architecture or follow an easy to use guide or tutorial in implementing the architecture. Once the programming aspect of the architecture is understood, I will then Implement a transformer based on the academic paper “Attention is All You Need”. I will then slightly tweak this model using my understanding of the architecture to improve performance. Once finished, the details (i.e., successes, failures, process and inner workings) of the implementation will be evaluated and reported, as well as the fundamental concepts surveyed. The motivation behind this project is to explore the rapidly growing area of AI algorithms, and the transformer algorithm in particular was chosen because it is a major milestone for engineering with AI and software. Since their introduction, transformers have provided a very effective way of solving natural language processing, which has allowed any related applications to succeed with high speed while maintaining accuracy. Since then, this type of model can be applied to more cutting edge natural language processing applications, such as extracting semantic information from a text description and generating an image to satisfy it.

ContributorsCereghini, Nicola (Author) / Acuna, Ruben (Thesis director) / Bansal, Ajay (Committee member) / Barrett, The Honors College (Contributor) / Software Engineering (Contributor)
Created2023-05
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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

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
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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

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
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Description
SLAM (Simultaneous Localization and Mapping) is a problem that has existed for a long time in robotics and autonomous navigation. The objective of SLAM is for a robot to simultaneously figure out its position in space and map its environment. SLAM is especially useful and mandatory for robots that want

SLAM (Simultaneous Localization and Mapping) is a problem that has existed for a long time in robotics and autonomous navigation. The objective of SLAM is for a robot to simultaneously figure out its position in space and map its environment. SLAM is especially useful and mandatory for robots that want to navigate autonomously. The description might make it seem like a chicken and egg problem, but numerous methods have been proposed to tackle SLAM. Before the rise in the popularity of deep learning and AI (Artificial Intelligence), most existing algorithms involved traditional hard-coded algorithms that would receive and process sensor information and convert it into some solvable sensor-agnostic problem. The challenge for these sorts of methods is having to tackle dynamic environments. The more variety in the environment, the poorer the results. Also due to the increase in computational power and the capability of deep learning-based image processing, visual SLAM has become extremely viable and maybe even preferable to traditional SLAM algorithms. In this research, a deep learning-based solution to the SLAM problem is proposed, specifically monocular visual SLAM which is solving the problem of SLAM purely with a singular camera as the input, and the model is tested on the KITTI (Karlsruhe Institute of Technology & Toyota Technological Institute) odometry dataset.
ContributorsRupaakula, Krishna Sandeep (Author) / Bansal, Ajay (Thesis advisor) / Baron, Tyler (Committee member) / Acuna, Ruben (Committee member) / Arizona State University (Publisher)
Created2023