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- All Subjects: Computer Science
- Creators: Baral, Chitta
Description
Reverse engineering gene regulatory networks (GRNs) is an important problem in the domain of Systems Biology. Learning GRNs is challenging due to the inherent complexity of the real regulatory networks and the heterogeneity of samples in available biomedical data. Real world biological data are commonly collected from broad surveys (profiling studies) and aggregate highly heterogeneous biological samples. Popular methods to learn GRNs simplistically assume a single universal regulatory network corresponding to available data. They neglect regulatory network adaptation due to change in underlying conditions and cellular phenotype or both. This dissertation presents a novel computational framework to learn common regulatory interactions and networks underlying the different sets of relatively homogeneous samples from real world biological data. The characteristic set of samples/conditions and corresponding regulatory interactions defines the cellular context (context). Context, in this dissertation, represents the deterministic transcriptional activity within the specific cellular regulatory mechanism. The major contributions of this framework include - modeling and learning context specific GRNs; associating enriched samples with contexts to interpret contextual interactions using biological knowledge; pruning extraneous edges from the context-specific GRN to improve the precision of the final GRNs; integrating multisource data to learn inter and intra domain interactions and increase confidence in obtained GRNs; and finally, learning combinatorial conditioning factors from the data to identify regulatory cofactors. The framework, Expattern, was applied to both real world and synthetic data. Interesting insights were obtained into mechanism of action of drugs on analysis of NCI60 drug activity and gene expression data. Application to refractory cancer data and Glioblastoma multiforme yield GRNs that were readily annotated with context-specific phenotypic information. Refractory cancer GRNs also displayed associations between distinct cancers, not observed through only clustering. Performance comparisons on multi-context synthetic data show the framework Expattern performs better than other comparable methods.
ContributorsSen, Ina (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Bittner, Michael (Committee member) / Konjevod, Goran (Committee member) / Arizona State University (Publisher)
Created2011
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
Different logic-based knowledge representation formalisms have different limitations either with respect to expressivity or with respect to computational efficiency. First-order logic, which is the basis of Description Logics (DLs), is not suitable for defeasible reasoning due to its monotonic nature. The nonmonotonic formalisms that extend first-order logic, such as circumscription and default logic, are expressive but lack efficient implementations. The nonmonotonic formalisms that are based on the declarative logic programming approach, such as Answer Set Programming (ASP), have efficient implementations but are not expressive enough for representing and reasoning with open domains. This dissertation uses the first-order stable model semantics, which extends both first-order logic and ASP, to relate circumscription to ASP, and to integrate DLs and ASP, thereby partially overcoming the limitations of the formalisms. By exploiting the relationship between circumscription and ASP, well-known action formalisms, such as the situation calculus, the event calculus, and Temporal Action Logics, are reformulated in ASP. The advantages of these reformulations are shown with respect to the generality of the reasoning tasks that can be handled and with respect to the computational efficiency. The integration of DLs and ASP presented in this dissertation provides a framework for integrating rules and ontologies for the semantic web. This framework enables us to perform nonmonotonic reasoning with DL knowledge bases. Observing the need to integrate action theories and ontologies, the above results are used to reformulate the problem of integrating action theories and ontologies as a problem of integrating rules and ontologies, thus enabling us to use the computational tools developed in the context of the latter for the former.
ContributorsPalla, Ravi (Author) / Lee, Joohyung (Thesis advisor) / Baral, Chitta (Committee member) / Kambhampati, Subbarao (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2012
Description
Automated planning problems classically involve finding a sequence of actions that transform an initial state to some state satisfying a conjunctive set of goals with no temporal constraints. But in many real-world problems, the best plan may involve satisfying only a subset of goals or missing defined goal deadlines. For example, this may be required when goals are logically conflicting, or when there are time or cost constraints such that achieving all goals on time may be too expensive. In this case, goals and deadlines must be declared as soft. I call these partial satisfaction planning (PSP) problems. In this work, I focus on particular types of PSP problems, where goals are given a quantitative value based on whether (or when) they are achieved. The objective is to find a plan with the best quality. A first challenge is in finding adequate goal representations that capture common types of goal achievement rewards and costs. One popular representation is to give a single reward on each goal of a planning problem. I further expand on this approach by allowing users to directly introduce utility dependencies, providing for changes of goal achievement reward directly based on the goals a plan achieves. After, I introduce time-dependent goal costs, where a plan incurs penalty if it will achieve a goal past a specified deadline. To solve PSP problems with goal utility dependencies, I look at using state-of-the-art methodologies currently employed for classical planning problems involving heuristic search. In doing so, one faces the challenge of simultaneously determining the best set of goals and plan to achieve them. This is complicated by utility dependencies defined by a user and cost dependencies within the plan. To address this, I introduce a set of heuristics based on combinations using relaxed plans and integer programming formulations. Further, I explore an approach to improve search through learning techniques by using automatically generated state features to find new states from which to search. Finally, the investigation into handling time-dependent goal costs leads us to an improved search technique derived from observations based on solving discretized approximations of cost functions.
ContributorsBenton, J (Author) / Kambhampati, Subbarao (Thesis advisor) / Baral, Chitta (Committee member) / Do, Minh B. (Committee member) / Smith, David E. (Committee member) / Langley, Pat (Committee member) / Arizona State University (Publisher)
Created2012
Description
While developing autonomous intelligent robots has been the goal of many research programs, a more practical application involving intelligent robots is the formation of teams consisting of both humans and robots. An example of such an application is search and rescue operations where robots commanded by humans are sent to environments too dangerous for humans. For such human-robot interaction, natural language is considered a good communication medium as it allows humans with less training about the robot's internal language to be able to command and interact with the robot. However, any natural language communication from the human needs to be translated to a formal language that the robot can understand. Similarly, before the robot can communicate (in natural language) with the human, it needs to formulate its communique in some formal language which then gets translated into natural language. In this paper, I develop a high level language for communication between humans and robots and demonstrate various aspects through a robotics simulation. These language constructs borrow some ideas from action execution languages and are grounded with respect to simulated human-robot interaction transcripts.
ContributorsLumpkin, Barry Thomas (Author) / Baral, Chitta (Thesis advisor) / Lee, Joohyung (Committee member) / Fainekos, Georgios (Committee member) / Arizona State University (Publisher)
Created2012
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
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
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
Teams are increasingly indispensable to achievements in any organizations. Despite the organizations' substantial dependency on teams, fundamental knowledge about the conduct of team-enabled operations is lacking, especially at the {\it social, cognitive} and {\it information} level in relation to team performance and network dynamics. The goal of this dissertation is to create new instruments to {\it predict}, {\it optimize} and {\it explain} teams' performance in the context of composite networks (i.e., social-cognitive-information networks).
Understanding the dynamic mechanisms that drive the success of high-performing teams can provide the key insights into building the best teams and hence lift the productivity and profitability of the organizations. For this purpose, novel predictive models to forecast the long-term performance of teams ({\it point prediction}) as well as the pathway to impact ({\it trajectory prediction}) have been developed. A joint predictive model by exploring the relationship between team level and individual level performances has also been proposed.
For an existing team, it is often desirable to optimize its performance through expanding the team by bringing a new team member with certain expertise, or finding a new candidate to replace an existing under-performing member. I have developed graph kernel based performance optimization algorithms by considering both the structural matching and skill matching to solve the above enhancement scenarios. I have also worked towards real time team optimization by leveraging reinforcement learning techniques.
With the increased complexity of the machine learning models for predicting and optimizing teams, it is critical to acquire a deeper understanding of model behavior. For this purpose, I have investigated {\em explainable prediction} -- to provide explanation behind a performance prediction and {\em explainable optimization} -- to give reasons why the model recommendations are good candidates for certain enhancement scenarios.
Understanding the dynamic mechanisms that drive the success of high-performing teams can provide the key insights into building the best teams and hence lift the productivity and profitability of the organizations. For this purpose, novel predictive models to forecast the long-term performance of teams ({\it point prediction}) as well as the pathway to impact ({\it trajectory prediction}) have been developed. A joint predictive model by exploring the relationship between team level and individual level performances has also been proposed.
For an existing team, it is often desirable to optimize its performance through expanding the team by bringing a new team member with certain expertise, or finding a new candidate to replace an existing under-performing member. I have developed graph kernel based performance optimization algorithms by considering both the structural matching and skill matching to solve the above enhancement scenarios. I have also worked towards real time team optimization by leveraging reinforcement learning techniques.
With the increased complexity of the machine learning models for predicting and optimizing teams, it is critical to acquire a deeper understanding of model behavior. For this purpose, I have investigated {\em explainable prediction} -- to provide explanation behind a performance prediction and {\em explainable optimization} -- to give reasons why the model recommendations are good candidates for certain enhancement scenarios.
ContributorsLi, Liangyue (Author) / Tong, Hanghang (Thesis advisor) / Baral, Chitta (Committee member) / Liu, Huan (Committee member) / Buchler, Norbou (Committee member) / Arizona State University (Publisher)
Created2018