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- All Subjects: knowledge representation
- Creators: Lee, Joohyung
Description
Biological organisms are made up of cells containing numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted, manifesting as disease symptoms. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for activities including diagnosing diseases and drug development. Scientists studying these interconnected processes have identified various pathways involved in drug metabolism, diseases, and signal transduction, etc. High-throughput technologies, new algorithms and speed improvements over the last decade have resulted in deeper knowledge about biological systems, leading to more refined pathways. Such pathways tend to be large and complex, making it difficult for an individual to remember all aspects. Thus, computer models are needed to represent and analyze them. The refinement activity itself requires reasoning with a pathway model by posing queries against it and comparing the results against the real biological system. Many existing models focus on structural and/or factoid questions, relying on surface-level information. These are generally not the kind of questions that a biologist may ask someone to test their understanding of biological processes. Examples of questions requiring understanding of biological processes are available in introductory college level biology text books. Such questions serve as a model for the question answering system developed in this thesis. Thus, the main goal of this thesis is to develop a system that allows the encoding of knowledge about biological pathways to answer questions demonstrating understanding of the pathways. To that end, a language is developed to specify a pathway and pose questions against it. Some existing tools are modified and used to accomplish this goal. The utility of the framework developed in this thesis is illustrated with applications in the biological domain. Finally, the question answering system is used in real world applications by extracting pathway knowledge from text and answering questions related to drug development.
ContributorsAnwar, Saadat (Author) / Baral, Chitta (Thesis advisor) / Inoue, Katsumi (Committee member) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Lee, Joohyung (Committee member) / Arizona State University (Publisher)
Created2014
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
Action language C+ is a formalism for describing properties of actions, which is based on nonmonotonic causal logic. The definite fragment of C+ is implemented in the Causal Calculator (CCalc), which is based on the reduction of nonmonotonic causal logic to propositional logic. This thesis describes the language of CCalc in terms of answer set programming (ASP), based on the translation of nonmonotonic causal logic to formulas under the stable model semantics. I designed a standard library which describes the constructs of the input language of CCalc in terms of ASP, allowing a simple modular method to represent CCalc input programs in the language of ASP. Using the combination of system F2LP and answer set solvers, this method achieves functionality close to that of CCalc while taking advantage of answer set solvers to yield efficient computation that is orders of magnitude faster than CCalc for many benchmark examples. In support of this, I created an automated translation system Cplus2ASP that implements the translation and encoding method and automatically invokes the necessary software to solve the translated input programs.
ContributorsCasolary, Michael (Author) / Lee, Joohyung (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2011
Description
The Web is one of the most exciting and dynamic areas of development in today’s technology. However, with such activity, innovation, and ubiquity have come a set of new challenges for digital forensic examiners, making their jobs even more difficult. For examiners to become as effective with evidence from the Web as they currently are with more traditional evidence, they need (1) methods that guide them to know how to approach this new type of evidence and (2) tools that accommodate web environments’ unique characteristics.
In this dissertation, I present my research to alleviate the difficulties forensic examiners currently face with respect to evidence originating from web environments. First, I introduce a framework for web environment forensics, which elaborates on and addresses the key challenges examiners face and outlines a method for how to approach web-based evidence. Next, I describe my work to identify extensions installed on encrypted web thin clients using only a sound understanding of these systems’ inner workings and the metadata of the encrypted files. Finally, I discuss my approach to reconstructing the timeline of events on encrypted web thin clients by using service provider APIs as a proxy for directly analyzing the device. In each of these research areas, I also introduce structured formats that I customized to accommodate the unique features of the evidence sources while also facilitating tool interoperability and information sharing.
In this dissertation, I present my research to alleviate the difficulties forensic examiners currently face with respect to evidence originating from web environments. First, I introduce a framework for web environment forensics, which elaborates on and addresses the key challenges examiners face and outlines a method for how to approach web-based evidence. Next, I describe my work to identify extensions installed on encrypted web thin clients using only a sound understanding of these systems’ inner workings and the metadata of the encrypted files. Finally, I discuss my approach to reconstructing the timeline of events on encrypted web thin clients by using service provider APIs as a proxy for directly analyzing the device. In each of these research areas, I also introduce structured formats that I customized to accommodate the unique features of the evidence sources while also facilitating tool interoperability and information sharing.
ContributorsMabey, Michael Kent (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Thesis advisor) / Yau, Stephen S. (Committee member) / Lee, Joohyung (Committee member) / Zhao, Ziming (Committee member) / Arizona State University (Publisher)
Created2017
Description
Reasoning about actions forms the basis of many tasks such as prediction, planning, and diagnosis in a dynamic domain. Within the reasoning about actions community, a broad class of languages, called action languages, has been developed together with a methodology for their use in representing and reasoning about dynamic domains. With a few notable exceptions, the focus of these efforts has largely centered around single-agent systems. Agents rarely operate in a vacuum however, and almost in parallel, substantial work has been done within the dynamic epistemic logic community towards understanding how the actions of an agent may effect not just his own knowledge and/or beliefs, but those of his fellow agents as well. What is less understood by both communities is how to represent and reason about both the direct and indirect effects of both ontic and epistemic actions within a multi-agent setting. This dissertation presents ongoing research towards a framework for representing and reasoning about dynamic multi-agent domains involving both classes of actions.
The contributions of this work are as follows: the formulation of a precise mathematical model of a dynamic multi-agent domain based on the notion of a transition diagram; the development of the multi-agent action languages mA+ and mAL based upon this model, as well as preliminary investigations of their properties and implementations via logic programming under the answer set semantics; precise formulations of the temporal projection, and planning problems within a multi-agent context; and an investigation of the application of the proposed approach to the representation of, and reasoning about, scenarios involving the modalities of knowledge and belief.
The contributions of this work are as follows: the formulation of a precise mathematical model of a dynamic multi-agent domain based on the notion of a transition diagram; the development of the multi-agent action languages mA+ and mAL based upon this model, as well as preliminary investigations of their properties and implementations via logic programming under the answer set semantics; precise formulations of the temporal projection, and planning problems within a multi-agent context; and an investigation of the application of the proposed approach to the representation of, and reasoning about, scenarios involving the modalities of knowledge and belief.
ContributorsGelfond, Gregory (Author) / Baral, Chitta (Thesis advisor) / Kambhampati, Subbarao (Committee member) / Lee, Joohyung (Committee member) / Moss, Larry (Committee member) / Cao Son, Tran (Committee member) / Arizona State University (Publisher)
Created2018
Description
Image Understanding is a long-established discipline in computer vision, which encompasses a body of advanced image processing techniques, that are used to locate (“where”), characterize and recognize (“what”) objects, regions, and their attributes in the image. However, the notion of “understanding” (and the goal of artificial intelligent machines) goes beyond factual recall of the recognized components and includes reasoning and thinking beyond what can be seen (or perceived). Understanding is often evaluated by asking questions of increasing difficulty. Thus, the expected functionalities of an intelligent Image Understanding system can be expressed in terms of the functionalities that are required to answer questions about an image. Answering questions about images require primarily three components: Image Understanding, question (natural language) understanding, and reasoning based on knowledge. Any question, asking beyond what can be directly seen, requires modeling of commonsense (or background/ontological/factual) knowledge and reasoning.
Knowledge and reasoning have seen scarce use in image understanding applications. In this thesis, we demonstrate the utilities of incorporating background knowledge and using explicit reasoning in image understanding applications. We first present a comprehensive survey of the previous work that utilized background knowledge and reasoning in understanding images. This survey outlines the limited use of commonsense knowledge in high-level applications. We then present a set of vision and reasoning-based methods to solve several applications and show that these approaches benefit in terms of accuracy and interpretability from the explicit use of knowledge and reasoning. We propose novel knowledge representations of image, knowledge acquisition methods, and a new implementation of an efficient probabilistic logical reasoning engine that can utilize publicly available commonsense knowledge to solve applications such as visual question answering, image puzzles. Additionally, we identify the need for new datasets that explicitly require external commonsense knowledge to solve. We propose the new task of Image Riddles, which requires a combination of vision, and reasoning based on ontological knowledge; and we collect a sufficiently large dataset to serve as an ideal testbed for vision and reasoning research. Lastly, we propose end-to-end deep architectures that can combine vision, knowledge and reasoning modules together and achieve large performance boosts over state-of-the-art methods.
Knowledge and reasoning have seen scarce use in image understanding applications. In this thesis, we demonstrate the utilities of incorporating background knowledge and using explicit reasoning in image understanding applications. We first present a comprehensive survey of the previous work that utilized background knowledge and reasoning in understanding images. This survey outlines the limited use of commonsense knowledge in high-level applications. We then present a set of vision and reasoning-based methods to solve several applications and show that these approaches benefit in terms of accuracy and interpretability from the explicit use of knowledge and reasoning. We propose novel knowledge representations of image, knowledge acquisition methods, and a new implementation of an efficient probabilistic logical reasoning engine that can utilize publicly available commonsense knowledge to solve applications such as visual question answering, image puzzles. Additionally, we identify the need for new datasets that explicitly require external commonsense knowledge to solve. We propose the new task of Image Riddles, which requires a combination of vision, and reasoning based on ontological knowledge; and we collect a sufficiently large dataset to serve as an ideal testbed for vision and reasoning research. Lastly, we propose end-to-end deep architectures that can combine vision, knowledge and reasoning modules together and achieve large performance boosts over state-of-the-art methods.
ContributorsAditya, Somak (Author) / Baral, Chitta (Thesis advisor) / Yang, Yezhou (Thesis advisor) / Aloimonos, Yiannis (Committee member) / Lee, Joohyung (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2018
Description
Knowledge Representation (KR) is one of the prominent approaches to Artificial Intelligence (AI) that is concerned with representing knowledge in a form that computer systems can utilize to solve complex problems. Answer Set Programming (ASP), based on the stable model semantics, is a widely-used KR framework that facilitates elegant and efficient representations for many problem domains that require complex reasoning.
However, while ASP is effective on deterministic problem domains, it is not suitable for applications involving quantitative uncertainty, for example, those that require probabilistic reasoning. Furthermore, it is hard to utilize information that can be statistically induced from data with ASP problem modeling.
This dissertation presents the language LP^MLN, which is a probabilistic extension of the stable model semantics with the concept of weighted rules, inspired by Markov Logic. An LP^MLN program defines a probability distribution over "soft" stable models, which may not satisfy all rules, but the more rules with the bigger weights they satisfy, the bigger their probabilities. LP^MLN takes advantage of both ASP and Markov Logic in a single framework, allowing representation of problems that require both logical and probabilistic reasoning in an intuitive and elaboration tolerant way.
This dissertation establishes formal relations between LP^MLN and several other formalisms, discusses inference and weight learning algorithms under LP^MLN, and presents systems implementing the algorithms. LP^MLN systems can be used to compute other languages translatable into LP^MLN.
The advantage of LP^MLN for probabilistic reasoning is illustrated by a probabilistic extension of the action language BC+, called pBC+, defined as a high-level notation of LP^MLN for describing transition systems. Various probabilistic reasoning about transition systems, especially probabilistic diagnosis, can be modeled in pBC+ and computed using LP^MLN systems. pBC+ is further extended with the notion of utility, through a decision-theoretic extension of LP^MLN, and related with Markov Decision Process (MDP) in terms of policy optimization problems. pBC+ can be used to represent (PO)MDP in a succinct and elaboration tolerant way, which enables planning with (PO)MDP algorithms in action domains whose description requires rich KR constructs, such as recursive definitions and indirect effects of actions.
However, while ASP is effective on deterministic problem domains, it is not suitable for applications involving quantitative uncertainty, for example, those that require probabilistic reasoning. Furthermore, it is hard to utilize information that can be statistically induced from data with ASP problem modeling.
This dissertation presents the language LP^MLN, which is a probabilistic extension of the stable model semantics with the concept of weighted rules, inspired by Markov Logic. An LP^MLN program defines a probability distribution over "soft" stable models, which may not satisfy all rules, but the more rules with the bigger weights they satisfy, the bigger their probabilities. LP^MLN takes advantage of both ASP and Markov Logic in a single framework, allowing representation of problems that require both logical and probabilistic reasoning in an intuitive and elaboration tolerant way.
This dissertation establishes formal relations between LP^MLN and several other formalisms, discusses inference and weight learning algorithms under LP^MLN, and presents systems implementing the algorithms. LP^MLN systems can be used to compute other languages translatable into LP^MLN.
The advantage of LP^MLN for probabilistic reasoning is illustrated by a probabilistic extension of the action language BC+, called pBC+, defined as a high-level notation of LP^MLN for describing transition systems. Various probabilistic reasoning about transition systems, especially probabilistic diagnosis, can be modeled in pBC+ and computed using LP^MLN systems. pBC+ is further extended with the notion of utility, through a decision-theoretic extension of LP^MLN, and related with Markov Decision Process (MDP) in terms of policy optimization problems. pBC+ can be used to represent (PO)MDP in a succinct and elaboration tolerant way, which enables planning with (PO)MDP algorithms in action domains whose description requires rich KR constructs, such as recursive definitions and indirect effects of actions.
ContributorsWang, Yi (Author) / Lee, Joohyung (Thesis advisor) / Baral, Chitta (Committee member) / Kambhampati, Subbarao (Committee member) / Natarajan, Sriraam (Committee member) / Srivastava, Siddharth (Committee member) / Arizona State University (Publisher)
Created2019
Description
Knowledge representation and reasoning is a prominent subject of study within the field of artificial intelligence that is concerned with the symbolic representation of knowledge in such a way to facilitate automated reasoning about this knowledge. Often in real-world domains, it is necessary to perform defeasible reasoning when representing default behaviors of systems. Answer Set Programming is a widely-used knowledge representation framework that is well-suited for such reasoning tasks and has been successfully applied to practical domains due to efficient computation through grounding--a process that replaces variables with variable-free terms--and propositional solvers similar to SAT solvers. However, some domains provide a challenge for grounding-based methods such as domains requiring reasoning about continuous time or resources.
To address these domains, there have been several proposals to achieve efficiency through loose integrations with efficient declarative solvers such as constraint solvers or satisfiability modulo theories solvers. While these approaches successfully avoid substantial grounding, due to the loose integration, they are not suitable for performing defeasible reasoning on functions. As a result, this expressive reasoning on functions must either be performed using predicates to simulate the functions or in a way that is not elaboration tolerant. Neither compromise is reasonable; the former suffers from the grounding bottleneck when domains are large as is often the case in real-world domains while the latter necessitates encodings to be non-trivially modified for elaborations.
This dissertation presents a novel framework called Answer Set Programming Modulo Theories (ASPMT) that is a tight integration of the stable model semantics and satisfiability modulo theories. This framework both supports defeasible reasoning about functions and alleviates the grounding bottleneck. Combining the strengths of Answer Set Programming and satisfiability modulo theories enables efficient continuous reasoning while still supporting rich reasoning features such as reasoning about defaults and reasoning in domains with incomplete knowledge. This framework is realized in two prototype implementations called MVSM and ASPMT2SMT, and the latter was recently incorporated into a non-monotonic spatial reasoning system. To define the semantics of this framework, we extend the first-order stable model semantics by Ferraris, Lee and Lifschitz to allow "intensional functions" and provide analyses of the theoretical properties of this new formalism and on the relationships between this and existing approaches.
To address these domains, there have been several proposals to achieve efficiency through loose integrations with efficient declarative solvers such as constraint solvers or satisfiability modulo theories solvers. While these approaches successfully avoid substantial grounding, due to the loose integration, they are not suitable for performing defeasible reasoning on functions. As a result, this expressive reasoning on functions must either be performed using predicates to simulate the functions or in a way that is not elaboration tolerant. Neither compromise is reasonable; the former suffers from the grounding bottleneck when domains are large as is often the case in real-world domains while the latter necessitates encodings to be non-trivially modified for elaborations.
This dissertation presents a novel framework called Answer Set Programming Modulo Theories (ASPMT) that is a tight integration of the stable model semantics and satisfiability modulo theories. This framework both supports defeasible reasoning about functions and alleviates the grounding bottleneck. Combining the strengths of Answer Set Programming and satisfiability modulo theories enables efficient continuous reasoning while still supporting rich reasoning features such as reasoning about defaults and reasoning in domains with incomplete knowledge. This framework is realized in two prototype implementations called MVSM and ASPMT2SMT, and the latter was recently incorporated into a non-monotonic spatial reasoning system. To define the semantics of this framework, we extend the first-order stable model semantics by Ferraris, Lee and Lifschitz to allow "intensional functions" and provide analyses of the theoretical properties of this new formalism and on the relationships between this and existing approaches.
ContributorsBartholomew, Michael James (Author) / Lee, Joohyung (Thesis advisor) / Bazzi, Rida (Committee member) / Colbourn, Charles (Committee member) / Fainekos, Georgios (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2016
Description
Several physical systems exist in the real world that involve continuous as well as discrete changes. These range from natural dynamic systems like the system of a bouncing ball to robotic dynamic systems such as planning the motion of a robot across obstacles. The key aspects of effectively describing such dynamic systems is to be able to plan and verify the evolution of the continuous components of the system while simultaneously maintaining critical constraints. Developing a framework that can effectively represent and find solutions to such physical systems prove to be highly advantageous. Both hybrid automata and action languages are formal models for describing the evolution of dynamic systems. The action language C+ is a rich and expressive language framework to formalize physical systems, but can be used only with physical systems in the discrete domain and is limited in its support of continuous domain components of such systems. Hybrid Automata is a well established formalism used to represent such complex physical systems at a theoretical level, however it is not expressive enough to capture the complex relations between the components of the system the way C+ does.
This thesis will focus on establishing a formal relationship between these two formalisms by showing how to succinctly represent Hybrid Automata in an action language which in turn is defined as a high-level notation for answer set programming modulo theories (ASPMT) --- an extension of answer set programs in the first-order level. Furthermore, this encoding framework is shown to be more effective and expressive than Hybrid Automata by highlighting its ability in allowing states of a hybrid transition system to be defined by complex relations among components that would otherwise be abstracted away in Hybrid Automata. The framework is further realized in the implementation of the system CPLUS2ASPMT, which takes advantage of state of the art ODE(Ordinary Differential Equations) based SMT solver dReal to provide support for ODE based evolution of continuous components of a dynamic system.
This thesis will focus on establishing a formal relationship between these two formalisms by showing how to succinctly represent Hybrid Automata in an action language which in turn is defined as a high-level notation for answer set programming modulo theories (ASPMT) --- an extension of answer set programs in the first-order level. Furthermore, this encoding framework is shown to be more effective and expressive than Hybrid Automata by highlighting its ability in allowing states of a hybrid transition system to be defined by complex relations among components that would otherwise be abstracted away in Hybrid Automata. The framework is further realized in the implementation of the system CPLUS2ASPMT, which takes advantage of state of the art ODE(Ordinary Differential Equations) based SMT solver dReal to provide support for ODE based evolution of continuous components of a dynamic system.
ContributorsLoney, Nikhil (Author) / Lee, Joohyung (Thesis advisor) / Fainekos, Georgios (Committee member) / Zhang, Yu (Committee member) / Arizona State University (Publisher)
Created2017
Description
Goal specification is an important aspect of designing autonomous agents. A goal does not only refer to the set of states for the agent to reach. A goal also defines restrictions on the paths the agent should follow. Temporal logics are widely used in goal specification. However, they lack the ability to represent goals in a non-deterministic domain, goals that change non-monotonically, and goals with preferences. This dissertation defines new goal specification languages by extending temporal logics to address these issues. First considered is the goal specification in non-deterministic domains, in which an agent following a policy leads to a set of paths. A logic is proposed to distinguish paths of the agent from all paths in the domain. In addition, to address the need of comparing policies for finding the best ones, a language capable of quantifying over policies is proposed. As policy structures of agents play an important role in goal specification, languages are also defined by considering different policy structures. Besides, after an agent is given an initial goal, the agent may change its expectations or the domain may change, thus goals that are previously specified may need to be further updated, revised, partially retracted, or even completely changed. Non-monotonic goal specification languages that can make these changes in an elaboration tolerant manner are needed. Two languages that rely on labeling sub-formulas and connecting multiple rules are developed to address non-monotonicity in goal specification. Also, agents may have preferential relations among sub-goals, and the preferential relations may change as agents achieve other sub-goals. By nesting a comparison operator with other temporal operators, a language with dynamic preferences is proposed. Various goals that cannot be expressed in other languages are expressed in the proposed languages. Finally, plans are given for some goals specified in the proposed languages.
ContributorsZhao, Jicheng (Author) / Baral, Chitta (Thesis advisor) / Kambhampati, Subbarao (Committee member) / Lee, Joohyung (Committee member) / Lifschitz, Vladimir (Committee member) / Liu, Huan (Committee member) / Arizona State University (Publisher)
Created2010