In this paper we present a language to reason about actions in a probabilistic setting and compar... more In this paper we present a language to reason about actions in a probabilistic setting and compare our work with earlier work by Pearl.The main feature of our language is its use of static and dynamic causal laws, and use of unknown (or background) variables - whose values are determined by factors beyond our model - in incorporating probabilities. We use two kind of unknown variables: inertial and non-inertial. Inertial unknown variables are helpful in assimilating observations and modeling counterfactuals and causality; while non-inertial unknown variables help characterize stochastic behavior, such as the outcome of tossing a coin, that are not impacted by observations. Finally, we give a glimpse of incorporating probabilities into reasoning with narratives.
Journal of the National Comprehensive Cancer Network, 2014
The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines ®) are a statement of consensu... more The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines ®) are a statement of consensus of the authors regarding their views of currently accepted approaches to treatment. The NCCN Guidelines ® Insights highlight important changes in the NCCN Guidelines ® recommendations from previous versions. Colored markings in the algorithm show changes and the discussion aims to further understanding of these changes by summarizing salient portions of the panel's discussion, including the literature reviewed. The NCCN Guidelines Insights do not represent the full NCCN Guidelines; further, the National Comprehensive Cancer Network ® (NCCN ®) makes no representation or warranties of any kind regarding the content, use, or application of the NCCN Guidelines and NCCN Guidelines Insights and disclaims any responsibility for their applications or use in any way. The full and most current version of these NCCN Guidelines are available at NCCN.org.
Journal of the National Comprehensive Cancer Network, 2011
All recommendations are Category 2A unless otherwise specified. The believes that the best manage... more All recommendations are Category 2A unless otherwise specified. The believes that the best management for any cancer patient is in a clinical trial. Participation in clinical trials is especially encouraged. NCCN To find clinical trials online at NCCN member institutions, click here: nccn.org/clinical_trials/physician.html See NCCN Categories of Evidence and Consensus The NCCN Guidelines are a statement of evidence and consensus of the authors regarding their views of currently accepted approaches to treatment. Any clinician seeking to apply or consult the NCCN Guidelines is expected to use independent medical judgment in the context of individual clinical circumstances to determine any patient's care or treatment.
Point of Care: The Journal of Near-Patient Testing & Technology, 2006
Abstract:We present two compendiums of point-of-care devices and rapid response tests available w... more Abstract:We present two compendiums of point-of-care devices and rapid response tests available worldwide. Information was gathered from both direct and indirect survey sources and crystallized into two tables, one a summary of POCT for mobile, emergency, critical, and primary care, and the other, a
The High Energy Physics Group at the University of Texas at Arlington has been developing a digit... more The High Energy Physics Group at the University of Texas at Arlington has been developing a digital hadron calorimeter (DHCAL) for future linear colliders using double-layer Gas Electron Multiplier (GEM) detector in the sensitive gap. The group has built prototype double GEM detectors in several sizes and have exposed four 30cm x 30cm prototype GEM detectors to particle beams at Fermi National Accelerator Laboratory. One of these detectors utilized a 13bit KPiX chip and its accompanying read out system developed at the Stanford Linear Accelerator Center. This talk will present the results of the beam test data analysis to understand the characteristics and performance of the prototype detectors. More specifically, it will present the measured gain, response, and efficiency of the detectors as well as the dependence of these quantities on the ambient pressure, position at which the particle passes through the detector and the applied high voltage.
IEEE Computer Society Bioinformatics Conference, 2003
We propose a formal language to represent and reason about signal transduction networks. The exis... more We propose a formal language to represent and reason about signal transduction networks. The existing approaches such as ones based on Petri nets, and π-calculus fall short in many ways and our work suggests that an artificial intelligence (AI) based approach may be well suited for many aspects. We apply a form of action language to represent and reason about
The first step in reasoning about actions and change involves reasoning about how the world would... more The first step in reasoning about actions and change involves reasoning about how the world would evolve if a certain action is executed in a certain state. Most research on this assume the evolution to be only a single step and focus on formulating the transition function that defines changes between states due to actions. In this paper we consider cases where the evolution is more than just a single change between one state and another. This is manifested when the execution of an action may trigger execution of other actions, or when multiple agents act on the environment following certain strategies.
The primary objective of this small-scale study was to investigate the occurrence of enteropathog... more The primary objective of this small-scale study was to investigate the occurrence of enteropathogens in sewage (municipal wastewater) in Norway using the commercially available FilmArray ® multiplex polymerase chain reaction (PCR) system with the gastrointestinal (GI) panel. Our findings indicate that DNA/RNA of several enteropathogens are present simultaneously in Norwegian wastewater systems. The spectre was broad even in smaller communities. With some exceptions, occurrence corresponded more or less to the reported cases of infectious human gastrointestinal disease in the same geographical regions. The effects of different sewage purification techniques were assessed on a limited number of samples indicating that neither chemical nor biological treatment was sufficiently effective to reduce gene material from the pathogens to undetectable levels. Further studies are required to assess the performance and suitability FilmArray ® multiplex PCR when used on collective sewage samples in outbreak situations. Additionally, screening sewage samples using multiplex-PCR could be valuable in order to detect new and emerging pathogens and for preliminary analysis of samples before proceeding to more work demanding confirmatory techniques.
Motivation: In this paper we propose to use recent developments in knowledge representation langu... more Motivation: In this paper we propose to use recent developments in knowledge representation languages and reasoning methodologies for representing and reasoning about signaling networks. Our approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation. Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations. Results: Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks. We use a NFÎşB related signaling pathway to illustrate the kinds of reasoning and representation that our system can currently do.
Motivation: The current knowledge about biochemical networks is largely incomplete. Thus biologis... more Motivation: The current knowledge about biochemical networks is largely incomplete. Thus biologists constantly need to revise or extend existing knowledge. The revision and/or extension are first formulated as theoretical hypotheses, then verified experimentally. Recently, biological data have been produced in great volumes and in diverse formats. It is a major challenge for biologists to process these data to reason about hypotheses. Many computer-aided systems have been developed to assist biologists in undertaking this challenge. The majority of the systems help in finding 'pattern' in data and leave the reasoning to biologists. A few systems have tried to automate the reasoning process of hypothesis formation. These systems generate hypotheses from a knowledge base and given observations. A main drawback of these knowledge-based systems is the knowledge representation formalisms they use. These formalisms are mostly monotonic and are now known to be not quite suitable for knowledge representation, especially in dealing with the inherently incomplete knowledge about biochemical networks. Results: We present a knowledge-based framework for hypothesis formation for biochemical networks. The framework has been implemented by extending BioSigNet-RR-a knowledge based system that supports elaboration-tolerant representation and non-monotonic reasoning. Features of the extended system are illustrated by a case study of the p53 signal network.
In this article we consider three different kinds of domain-dependent control knowledge (temporal... more In this article we consider three different kinds of domain-dependent control knowledge (temporal, procedural and HTN-based) that are useful in planning. Our approach is declarative and relies on the language of logic programming with answer set semantics (AnsProlog*). AnsProlog* is designed to plan without control knowledge. We show how temporal, procedural and HTN-based control knowledge can be incorporated into AnsProlog* by the modular addition of a small number of domain-dependent rules, without the need to modify the planner. We formally prove the correctness of our planner, both in the absence and presence of the control knowledge. Finally, we perform some initial experimentation that demonstrates the potential reduction in planning time that can be achieved when procedural domain knowledge is used to solve planning problems with large plan length.
In this paper, we consider the problem of planning with temporal goals, focussing on polynomially... more In this paper, we consider the problem of planning with temporal goals, focussing on polynomially bounded length plans. Past results about complexity of planning are mostly about finding plans that take the world to one of several desired states, often described using a goal formula. We first consider goals expressed using linear temporal logic and analyze the complexity of planning with respect to such goals for both when the states in the trajectory are complete states, and when they are incomplete states. For the later case we ...
Nonmonotonic Reasoning, Action, and Change (NRAC’03), 2003
Pearl's probabilistic causal model has been used in many domains to reason about causality. ... more Pearl's probabilistic causal model has been used in many domains to reason about causality. Pearl's treatment of actions is very different from the way actions are represented (explicitly) and their impact is reasoned in most other papers in the literature. In this paper we show how to encode Pearl's probabilistic causal model in the action language PAL thus relating this two distinct approaches to reason about actions.
PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE, Jul 25, 2004
Pearl's probabilistic causal model has been used in many domains to reason about causality. ... more Pearl's probabilistic causal model has been used in many domains to reason about causality. Pearl's treatment of actions is very different from the way actions are represented explicitly in action languages. In this paper we show how to encode Pearl's probabilistic causal model in the action language PAL thus relating this two distinct approaches to reasoning about actions.
Proceedings of the Third International Conference on Computational Methods in System Biology (CMSB 2005), 2005
Abstract. We present a simple signal transduction pathway from the literature, modelled using a k... more Abstract. We present a simple signal transduction pathway from the literature, modelled using a knowledge-based approach in the tool BioSigNet-RR. This allows qualitative analysis of the pathway in three ways. Keywords: signal transduction pathways, knowledge representation.
In this paper we present a language to reason about actions in a probabilistic setting and compar... more In this paper we present a language to reason about actions in a probabilistic setting and compare our work with earlier work by Pearl.The main feature of our language is its use of static and dynamic causal laws, and use of unknown (or background) variables - whose values are determined by factors beyond our model - in incorporating probabilities. We use two kind of unknown variables: inertial and non-inertial. Inertial unknown variables are helpful in assimilating observations and modeling counterfactuals and causality; while non-inertial unknown variables help characterize stochastic behavior, such as the outcome of tossing a coin, that are not impacted by observations. Finally, we give a glimpse of incorporating probabilities into reasoning with narratives.
Journal of the National Comprehensive Cancer Network, 2014
The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines ®) are a statement of consensu... more The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines ®) are a statement of consensus of the authors regarding their views of currently accepted approaches to treatment. The NCCN Guidelines ® Insights highlight important changes in the NCCN Guidelines ® recommendations from previous versions. Colored markings in the algorithm show changes and the discussion aims to further understanding of these changes by summarizing salient portions of the panel's discussion, including the literature reviewed. The NCCN Guidelines Insights do not represent the full NCCN Guidelines; further, the National Comprehensive Cancer Network ® (NCCN ®) makes no representation or warranties of any kind regarding the content, use, or application of the NCCN Guidelines and NCCN Guidelines Insights and disclaims any responsibility for their applications or use in any way. The full and most current version of these NCCN Guidelines are available at NCCN.org.
Journal of the National Comprehensive Cancer Network, 2011
All recommendations are Category 2A unless otherwise specified. The believes that the best manage... more All recommendations are Category 2A unless otherwise specified. The believes that the best management for any cancer patient is in a clinical trial. Participation in clinical trials is especially encouraged. NCCN To find clinical trials online at NCCN member institutions, click here: nccn.org/clinical_trials/physician.html See NCCN Categories of Evidence and Consensus The NCCN Guidelines are a statement of evidence and consensus of the authors regarding their views of currently accepted approaches to treatment. Any clinician seeking to apply or consult the NCCN Guidelines is expected to use independent medical judgment in the context of individual clinical circumstances to determine any patient's care or treatment.
Point of Care: The Journal of Near-Patient Testing & Technology, 2006
Abstract:We present two compendiums of point-of-care devices and rapid response tests available w... more Abstract:We present two compendiums of point-of-care devices and rapid response tests available worldwide. Information was gathered from both direct and indirect survey sources and crystallized into two tables, one a summary of POCT for mobile, emergency, critical, and primary care, and the other, a
The High Energy Physics Group at the University of Texas at Arlington has been developing a digit... more The High Energy Physics Group at the University of Texas at Arlington has been developing a digital hadron calorimeter (DHCAL) for future linear colliders using double-layer Gas Electron Multiplier (GEM) detector in the sensitive gap. The group has built prototype double GEM detectors in several sizes and have exposed four 30cm x 30cm prototype GEM detectors to particle beams at Fermi National Accelerator Laboratory. One of these detectors utilized a 13bit KPiX chip and its accompanying read out system developed at the Stanford Linear Accelerator Center. This talk will present the results of the beam test data analysis to understand the characteristics and performance of the prototype detectors. More specifically, it will present the measured gain, response, and efficiency of the detectors as well as the dependence of these quantities on the ambient pressure, position at which the particle passes through the detector and the applied high voltage.
IEEE Computer Society Bioinformatics Conference, 2003
We propose a formal language to represent and reason about signal transduction networks. The exis... more We propose a formal language to represent and reason about signal transduction networks. The existing approaches such as ones based on Petri nets, and π-calculus fall short in many ways and our work suggests that an artificial intelligence (AI) based approach may be well suited for many aspects. We apply a form of action language to represent and reason about
The first step in reasoning about actions and change involves reasoning about how the world would... more The first step in reasoning about actions and change involves reasoning about how the world would evolve if a certain action is executed in a certain state. Most research on this assume the evolution to be only a single step and focus on formulating the transition function that defines changes between states due to actions. In this paper we consider cases where the evolution is more than just a single change between one state and another. This is manifested when the execution of an action may trigger execution of other actions, or when multiple agents act on the environment following certain strategies.
The primary objective of this small-scale study was to investigate the occurrence of enteropathog... more The primary objective of this small-scale study was to investigate the occurrence of enteropathogens in sewage (municipal wastewater) in Norway using the commercially available FilmArray ® multiplex polymerase chain reaction (PCR) system with the gastrointestinal (GI) panel. Our findings indicate that DNA/RNA of several enteropathogens are present simultaneously in Norwegian wastewater systems. The spectre was broad even in smaller communities. With some exceptions, occurrence corresponded more or less to the reported cases of infectious human gastrointestinal disease in the same geographical regions. The effects of different sewage purification techniques were assessed on a limited number of samples indicating that neither chemical nor biological treatment was sufficiently effective to reduce gene material from the pathogens to undetectable levels. Further studies are required to assess the performance and suitability FilmArray ® multiplex PCR when used on collective sewage samples in outbreak situations. Additionally, screening sewage samples using multiplex-PCR could be valuable in order to detect new and emerging pathogens and for preliminary analysis of samples before proceeding to more work demanding confirmatory techniques.
Motivation: In this paper we propose to use recent developments in knowledge representation langu... more Motivation: In this paper we propose to use recent developments in knowledge representation languages and reasoning methodologies for representing and reasoning about signaling networks. Our approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation. Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations. Results: Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks. We use a NFÎşB related signaling pathway to illustrate the kinds of reasoning and representation that our system can currently do.
Motivation: The current knowledge about biochemical networks is largely incomplete. Thus biologis... more Motivation: The current knowledge about biochemical networks is largely incomplete. Thus biologists constantly need to revise or extend existing knowledge. The revision and/or extension are first formulated as theoretical hypotheses, then verified experimentally. Recently, biological data have been produced in great volumes and in diverse formats. It is a major challenge for biologists to process these data to reason about hypotheses. Many computer-aided systems have been developed to assist biologists in undertaking this challenge. The majority of the systems help in finding 'pattern' in data and leave the reasoning to biologists. A few systems have tried to automate the reasoning process of hypothesis formation. These systems generate hypotheses from a knowledge base and given observations. A main drawback of these knowledge-based systems is the knowledge representation formalisms they use. These formalisms are mostly monotonic and are now known to be not quite suitable for knowledge representation, especially in dealing with the inherently incomplete knowledge about biochemical networks. Results: We present a knowledge-based framework for hypothesis formation for biochemical networks. The framework has been implemented by extending BioSigNet-RR-a knowledge based system that supports elaboration-tolerant representation and non-monotonic reasoning. Features of the extended system are illustrated by a case study of the p53 signal network.
In this article we consider three different kinds of domain-dependent control knowledge (temporal... more In this article we consider three different kinds of domain-dependent control knowledge (temporal, procedural and HTN-based) that are useful in planning. Our approach is declarative and relies on the language of logic programming with answer set semantics (AnsProlog*). AnsProlog* is designed to plan without control knowledge. We show how temporal, procedural and HTN-based control knowledge can be incorporated into AnsProlog* by the modular addition of a small number of domain-dependent rules, without the need to modify the planner. We formally prove the correctness of our planner, both in the absence and presence of the control knowledge. Finally, we perform some initial experimentation that demonstrates the potential reduction in planning time that can be achieved when procedural domain knowledge is used to solve planning problems with large plan length.
In this paper, we consider the problem of planning with temporal goals, focussing on polynomially... more In this paper, we consider the problem of planning with temporal goals, focussing on polynomially bounded length plans. Past results about complexity of planning are mostly about finding plans that take the world to one of several desired states, often described using a goal formula. We first consider goals expressed using linear temporal logic and analyze the complexity of planning with respect to such goals for both when the states in the trajectory are complete states, and when they are incomplete states. For the later case we ...
Nonmonotonic Reasoning, Action, and Change (NRAC’03), 2003
Pearl's probabilistic causal model has been used in many domains to reason about causality. ... more Pearl's probabilistic causal model has been used in many domains to reason about causality. Pearl's treatment of actions is very different from the way actions are represented (explicitly) and their impact is reasoned in most other papers in the literature. In this paper we show how to encode Pearl's probabilistic causal model in the action language PAL thus relating this two distinct approaches to reason about actions.
PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE, Jul 25, 2004
Pearl's probabilistic causal model has been used in many domains to reason about causality. ... more Pearl's probabilistic causal model has been used in many domains to reason about causality. Pearl's treatment of actions is very different from the way actions are represented explicitly in action languages. In this paper we show how to encode Pearl's probabilistic causal model in the action language PAL thus relating this two distinct approaches to reasoning about actions.
Proceedings of the Third International Conference on Computational Methods in System Biology (CMSB 2005), 2005
Abstract. We present a simple signal transduction pathway from the literature, modelled using a k... more Abstract. We present a simple signal transduction pathway from the literature, modelled using a knowledge-based approach in the tool BioSigNet-RR. This allows qualitative analysis of the pathway in three ways. Keywords: signal transduction pathways, knowledge representation.
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