Matching Items (24)
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- All Subjects: Machine Learning
- Creators: Papandreou-Suppappola, Antonia
- Creators: Baral, Chitta
- Member of: ASU Electronic Theses and Dissertations
Description
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
Description
The advancement and marked increase in the use of computing devices in health care for large scale and personal medical use has transformed the field of medicine and health care into a data rich domain. This surge in the availability of data has allowed domain experts to investigate, study and discover inherent patterns in diseases from new perspectives and in turn, further the field of medicine. Storage and analysis of this data in real time aids in enhancing the response time and efficiency of doctors and health care specialists. However, due to the time critical nature of most life- threatening diseases, there is a growing need to make informed decisions prior to the occurrence of any fatal outcome. Alongside time sensitivity, analyzing data specific to diseases and their effects on an individual basis leads to more efficient prognosis and rapid deployment of cures. The primary challenge in addressing both of these issues arises from the time varying and time sensitive nature of the data being studied and in the ability to successfully predict anomalous events using only observed data.This dissertation introduces adaptive machine learning algorithms that aid in the prediction of anomalous situations arising due to abnormalities present in patients diagnosed with certain types of diseases. Emphasis is given to the adaptation and development of algorithms based on an individual basis to further the accuracy of all predictions made. The main objectives are to learn the underlying representation of the data using empirical methods and enhance it using domain knowledge. The learned model is then utilized as a guide for statistical machine learning methods to predict the occurrence of anomalous events in the near future. Further enhancement of the learned model is achieved by means of tuning the objective function of the algorithm to incorporate domain knowledge. Along with anomaly forecasting using multi-modal data, this dissertation also investigates the use of univariate time series data towards the prediction of onset of diseases using Bayesian nonparametrics.
ContributorsDas, Subhasish (Author) / Gupta, Sandeep K.S. (Thesis advisor) / Banerjee, Ayan (Committee member) / Indic, Premananda (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2022
Description
Multi-segment manipulators and mobile robot collectives are examples of multi-agent robotic systems, in which each segment or robot can be considered an agent. Fundamental motion control problems for such systems include the stabilization of one or more agents to target configurations or trajectories while preventing inter-agent collisions, agent collisions with obstacles, and deadlocks. Despite extensive research on these control problems, there are still challenges in designing controllers that (1) are scalable with the number of agents; (2) have theoretical guarantees on collision-free agent navigation; and (3) can be used when the states of the agents and the environment are only partially observable. Existing centralized and distributed control architectures have limited scalability due to their computational complexity and communication requirements, while decentralized control architectures are often effective only under impractical assumptions that do not hold in real-world implementations. The main objective of this dissertation is to develop and evaluate decentralized approaches for multi-agent motion control that enable agents to use their onboard sensors and computational resources to decide how to move through their environment, with limited or absent inter-agent communication and external supervision. Specifically, control approaches are designed for multi-segment manipulators and mobile robot collectives to achieve position and pose (position and orientation) stabilization, trajectory tracking, and collision and deadlock avoidance. These control approaches are validated in both simulations and physical experiments to show that they can be implemented in real-time while remaining computationally tractable. First, kinematic controllers are proposed for position stabilization and trajectory tracking control of two- or three-dimensional hyper-redundant multi-segment manipulators. Next, robust and gradient-based feedback controllers are presented for individual holonomic and nonholonomic mobile robots that achieve position stabilization, trajectory tracking control, and obstacle avoidance. Then, nonlinear Model Predictive Control methods are developed for collision-free, deadlock-free pose stabilization and trajectory tracking control of multiple nonholonomic mobile robots in known and unknown environments with obstacles, both static and dynamic. Finally, a feedforward proportional-derivative controller is defined for collision-free velocity tracking of a moving ground target by multiple unmanned aerial vehicles.
ContributorsSalimi Lafmejani, Amir (Author) / Berman, Spring (Thesis advisor) / Tsakalis, Konstantinos (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Marvi, Hamidreza (Committee member) / Arizona State University (Publisher)
Created2022
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
Predicting nonlinear dynamical systems has been a long-standing challenge in science. This field is currently witnessing a revolution with the advent of machine learning methods. Concurrently, the analysis of dynamics in various nonlinear complex systems continues to be crucial. Guided by these directions, I conduct the following studies. Predicting critical transitions and transient states in nonlinear dynamics is a complex problem. I developed a solution called parameter-aware reservoir computing, which uses machine learning to track how system dynamics change with a driving parameter. I show that the transition point can be accurately predicted while trained in a sustained functioning regime before the transition. Notably, it can also predict if the system will enter a transient state, the distribution of transient lifetimes, and their average before a final collapse, which are crucial for management. I introduce a machine-learning-based digital twin for monitoring and predicting the evolution of externally driven nonlinear dynamical systems, where reservoir computing is exploited. Extensive tests on various models, encompassing optics, ecology, and climate, verify the approach’s effectiveness. The digital twins can extrapolate unknown system dynamics, continually forecast and monitor under non-stationary external driving, infer hidden variables, adapt to different driving waveforms, and extrapolate bifurcation behaviors across varying system sizes. Integrating engineered gene circuits into host cells poses a significant challenge in synthetic biology due to circuit-host interactions, such as growth feedback. I conducted systematic studies on hundreds of circuit structures exhibiting various functionalities, and identified a comprehensive categorization of growth-induced failures. I discerned three dynamical mechanisms behind these circuit failures. Moreover, my comprehensive computations reveal a scaling law between the circuit robustness and the intensity of growth feedback. A class of circuits with optimal robustness is also identified. Chimera states, a phenomenon of symmetry-breaking in oscillator networks, traditionally have transient lifetimes that grow exponentially with system size. However, my research on high-dimensional oscillators leads to the discovery of ’short-lived’ chimera states. Their lifetime increases logarithmically with system size and decreases logarithmically with random perturbations, indicating a unique fragility. To understand these states, I use a transverse stability analysis supported by simulations.
ContributorsKong, Lingwei (Author) / Lai, Ying-Cheng (Thesis advisor) / Tian, Xiaojun (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Alkhateeb, Ahmed (Committee member) / Arizona State University (Publisher)
Created2023
Description
Models that learn from data are widely and rapidly being deployed today for real-world use, and have become an integral and embedded part of human lives. While these technological advances are exciting and impactful, such data-driven computer vision systems often fail in inscrutable ways. This dissertation seeks to study and improve the reliability of machine learning models from several perspectives including the development of robust training algorithms to mitigate the risks of such failures, construction of new datasets that provide a new perspective on capabilities of vision models, and the design of evaluation metrics for re-calibrating the perception of performance improvements. I will first address distribution shift in image classification with the following contributions: (1) two methods for improving the robustness of image classifiers to distribution shift by leveraging the classifier's failures into an adversarial data transformation pipeline guided by domain knowledge, (2) an interpolation-based technique for flagging out-of-distribution samples, and (3) an intriguing trade-off between distributional and adversarial robustness resulting from data modification strategies. I will then explore reliability considerations for \textit{semantic vision} models that learn from both visual and natural language data; I will discuss how logical and semantic sentence transformations affect the performance of vision--language models and my contributions towards developing knowledge-guided learning algorithms to mitigate these failures. Finally, I will describe the effort towards building and evaluating complex reasoning capabilities of vision--language models towards the long-term goal of robust and reliable computer vision models that can communicate, collaborate, and reason with humans.
ContributorsGokhale, Tejas (Author) / Yang, Yezhou (Thesis advisor) / Baral, Chitta (Thesis advisor) / Ben Amor, Heni (Committee member) / Anirudh, Rushil (Committee member) / Arizona State University (Publisher)
Created2023
Description
Reasoning about the activities of cyber threat actors is critical to defend against cyber
attacks. However, this task is difficult for a variety of reasons. In simple terms, it is difficult
to determine who the attacker is, what the desired goals are of the attacker, and how they will
carry out their attacks. These three questions essentially entail understanding the attacker’s
use of deception, the capabilities available, and the intent of launching the attack. These
three issues are highly inter-related. If an adversary can hide their intent, they can better
deceive a defender. If an adversary’s capabilities are not well understood, then determining
what their goals are becomes difficult as the defender is uncertain if they have the necessary
tools to accomplish them. However, the understanding of these aspects are also mutually
supportive. If we have a clear picture of capabilities, intent can better be deciphered. If we
understand intent and capabilities, a defender may be able to see through deception schemes.
In this dissertation, I present three pieces of work to tackle these questions to obtain
a better understanding of cyber threats. First, we introduce a new reasoning framework
to address deception. We evaluate the framework by building a dataset from DEFCON
capture-the-flag exercise to identify the person or group responsible for a cyber attack.
We demonstrate that the framework not only handles cases of deception but also provides
transparent decision making in identifying the threat actor. The second task uses a cognitive
learning model to determine the intent – goals of the threat actor on the target system.
The third task looks at understanding the capabilities of threat actors to target systems by
identifying at-risk systems from hacker discussions on darkweb websites. To achieve this
task we gather discussions from more than 300 darkweb websites relating to malicious
hacking.
attacks. However, this task is difficult for a variety of reasons. In simple terms, it is difficult
to determine who the attacker is, what the desired goals are of the attacker, and how they will
carry out their attacks. These three questions essentially entail understanding the attacker’s
use of deception, the capabilities available, and the intent of launching the attack. These
three issues are highly inter-related. If an adversary can hide their intent, they can better
deceive a defender. If an adversary’s capabilities are not well understood, then determining
what their goals are becomes difficult as the defender is uncertain if they have the necessary
tools to accomplish them. However, the understanding of these aspects are also mutually
supportive. If we have a clear picture of capabilities, intent can better be deciphered. If we
understand intent and capabilities, a defender may be able to see through deception schemes.
In this dissertation, I present three pieces of work to tackle these questions to obtain
a better understanding of cyber threats. First, we introduce a new reasoning framework
to address deception. We evaluate the framework by building a dataset from DEFCON
capture-the-flag exercise to identify the person or group responsible for a cyber attack.
We demonstrate that the framework not only handles cases of deception but also provides
transparent decision making in identifying the threat actor. The second task uses a cognitive
learning model to determine the intent – goals of the threat actor on the target system.
The third task looks at understanding the capabilities of threat actors to target systems by
identifying at-risk systems from hacker discussions on darkweb websites. To achieve this
task we gather discussions from more than 300 darkweb websites relating to malicious
hacking.
ContributorsNunes, Eric (Author) / Shakarian, Paulo (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Cooke, Nancy J. (Committee member) / Arizona State University (Publisher)
Created2018
Description
Disentangling latent spaces is an important research direction in the interpretability of unsupervised machine learning. Several recent works using deep learning are very effective at producing disentangled representations. However, in the unsupervised setting, there is no way to pre-specify which part of the latent space captures specific factors of variations. While this is generally a hard problem because of the non-existence of analytical expressions to capture these variations, there are certain factors like geometric
transforms that can be expressed analytically. Furthermore, in existing frameworks, the disentangled values are also not interpretable. The focus of this work is to disentangle these geometric factors of variations (which turn out to be nuisance factors for many applications) from the semantic content of the signal in an interpretable manner which in turn makes the features more discriminative. Experiments are designed to show the modularity of the approach with other disentangling strategies as well as on multiple one-dimensional (1D) and two-dimensional (2D) datasets, clearly indicating the efficacy of the proposed approach.
transforms that can be expressed analytically. Furthermore, in existing frameworks, the disentangled values are also not interpretable. The focus of this work is to disentangle these geometric factors of variations (which turn out to be nuisance factors for many applications) from the semantic content of the signal in an interpretable manner which in turn makes the features more discriminative. Experiments are designed to show the modularity of the approach with other disentangling strategies as well as on multiple one-dimensional (1D) and two-dimensional (2D) datasets, clearly indicating the efficacy of the proposed approach.
ContributorsKoneripalli Seetharam, Kaushik (Author) / Turaga, Pavan (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Jayasuriya, Suren (Committee member) / Arizona State University (Publisher)
Created2019
Description
Deep learning (DL) has proved itself be one of the most important developements till date with far reaching impacts in numerous fields like robotics, computer vision, surveillance, speech processing, machine translation, finance, etc. They are now widely used for countless applications because of their ability to generalize real world data, robustness to noise in previously unseen data and high inference accuracy. With the ability to learn useful features from raw sensor data, deep learning algorithms have out-performed tradinal AI algorithms and pushed the boundaries of what can be achieved with AI. In this work, we demonstrate the power of deep learning by developing a neural network to automatically detect cough instances from audio recorded in un-constrained environments. For this, 24 hours long recordings from 9 dierent patients is collected and carefully labeled by medical personel. A pre-processing algorithm is proposed to convert event based cough dataset to a more informative dataset with start and end of coughs and also introduce data augmentation for regularizing the training procedure. The proposed neural network achieves 92.3% leave-one-out accuracy on data captured in real world.
Deep neural networks are composed of multiple layers that are compute/memory intensive. This makes it difficult to execute these algorithms real-time with low power consumption using existing general purpose computers. In this work, we propose hardware accelerators for a traditional AI algorithm based on random forest trees and two representative deep convolutional neural networks (AlexNet and VGG). With the proposed acceleration techniques, ~ 30x performance improvement was achieved compared to CPU for random forest trees. For deep CNNS, we demonstrate that much higher performance can be achieved with architecture space exploration using any optimization algorithms with system level performance and area models for hardware primitives as inputs and goal of minimizing latency with given resource constraints. With this method, ~30GOPs performance was achieved for Stratix V FPGA boards.
Hardware acceleration of DL algorithms alone is not always the most ecient way and sucient to achieve desired performance. There is a huge headroom available for performance improvement provided the algorithms are designed keeping in mind the hardware limitations and bottlenecks. This work achieves hardware-software co-optimization for Non-Maximal Suppression (NMS) algorithm. Using the proposed algorithmic changes and hardware architecture
With CMOS scaling coming to an end and increasing memory bandwidth bottlenecks, CMOS based system might not scale enough to accommodate requirements of more complicated and deeper neural networks in future. In this work, we explore RRAM crossbars and arrays as compact, high performing and energy efficient alternative to CMOS accelerators for deep learning training and inference. We propose and implement RRAM periphery read and write circuits and achieved ~3000x performance improvement in online dictionary learning compared to CPU.
This work also examines the realistic RRAM devices and their non-idealities. We do an in-depth study of the effects of RRAM non-idealities on inference accuracy when a pretrained model is mapped to RRAM based accelerators. To mitigate this issue, we propose Random Sparse Adaptation (RSA), a novel scheme aimed at tuning the model to take care of the faults of the RRAM array on which it is mapped. Our proposed method can achieve inference accuracy much higher than what traditional Read-Verify-Write (R-V-W) method could achieve. RSA can also recover lost inference accuracy 100x ~ 1000x faster compared to R-V-W. Using 32-bit high precision RSA cells, we achieved ~10% higher accuracy using fautly RRAM arrays compared to what can be achieved by mapping a deep network to an 32 level RRAM array with no variations.
Deep neural networks are composed of multiple layers that are compute/memory intensive. This makes it difficult to execute these algorithms real-time with low power consumption using existing general purpose computers. In this work, we propose hardware accelerators for a traditional AI algorithm based on random forest trees and two representative deep convolutional neural networks (AlexNet and VGG). With the proposed acceleration techniques, ~ 30x performance improvement was achieved compared to CPU for random forest trees. For deep CNNS, we demonstrate that much higher performance can be achieved with architecture space exploration using any optimization algorithms with system level performance and area models for hardware primitives as inputs and goal of minimizing latency with given resource constraints. With this method, ~30GOPs performance was achieved for Stratix V FPGA boards.
Hardware acceleration of DL algorithms alone is not always the most ecient way and sucient to achieve desired performance. There is a huge headroom available for performance improvement provided the algorithms are designed keeping in mind the hardware limitations and bottlenecks. This work achieves hardware-software co-optimization for Non-Maximal Suppression (NMS) algorithm. Using the proposed algorithmic changes and hardware architecture
With CMOS scaling coming to an end and increasing memory bandwidth bottlenecks, CMOS based system might not scale enough to accommodate requirements of more complicated and deeper neural networks in future. In this work, we explore RRAM crossbars and arrays as compact, high performing and energy efficient alternative to CMOS accelerators for deep learning training and inference. We propose and implement RRAM periphery read and write circuits and achieved ~3000x performance improvement in online dictionary learning compared to CPU.
This work also examines the realistic RRAM devices and their non-idealities. We do an in-depth study of the effects of RRAM non-idealities on inference accuracy when a pretrained model is mapped to RRAM based accelerators. To mitigate this issue, we propose Random Sparse Adaptation (RSA), a novel scheme aimed at tuning the model to take care of the faults of the RRAM array on which it is mapped. Our proposed method can achieve inference accuracy much higher than what traditional Read-Verify-Write (R-V-W) method could achieve. RSA can also recover lost inference accuracy 100x ~ 1000x faster compared to R-V-W. Using 32-bit high precision RSA cells, we achieved ~10% higher accuracy using fautly RRAM arrays compared to what can be achieved by mapping a deep network to an 32 level RRAM array with no variations.
ContributorsMohanty, Abinash (Author) / Cao, Yu (Thesis advisor) / Seo, Jae-Sun (Committee member) / Vrudhula, Sarma (Committee member) / Chakrabarti, Chaitali (Committee member) / Arizona State University (Publisher)
Created2018