ChemReasoner - Catalyst Discovery via Large Language Model-driven Reasoning( 32832-E)
ChemReasoner - Catalyst Discovery via Large Language Model-driven Reasoning
Choudhury, Sutanay [Pacific Northwest National Lab↗
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Improving ontologies by automatic reasoning and evaluation of logical definitions
Background: Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly being adopted as a method for quality control as well as for facilitating interoperability and data integration. Results: We show how automated reasoning over logical definitions of ontology terms can be used to improve ontology structure. We provide the Java software package GULO (Getting an Understanding of LOgical definitions), which allows fast and easy evaluation for any kind of logically decomposed ontology by generating a composite OWL ontology from appropriate subsets of the referenced ontologies and comparing the inferred relationships with the relationships asserted in the target ontology. As a case study we show how to use GULO to evaluate the logical definitions that have been developed for the Mammalian Phenotype Ontology (MPO). Conclusions: Logical definitions of terms from biomedical ontologies represent an important resource for error and disagreement detection. GULO gives ontology curators a fast and simple tool for validation of their work.
59 BASIC BIOLOGICAL SCIENCES↗
PHYSICS-BASED AUTOMATED REASONING FOR HEALTH MONITORING: SENSOR SET SELECTION
This paper addresses the problem of how to select a sensor set for equipment health monitoring that meets the needs of advanced O&M tasks that target cost reduction. They include maintenance optimization and asset management for the existing fleet and near-autonomous operation as currently envisioned for advanced reactors. The method uses physics-based automated reasoning to provide for a more “explainable” diagnosis. The algorithm is described along with its implementation on a computational cluster. Preliminary results for application to a use case in the current fleet are described.
diagnosis↗
Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study
Development of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials. A modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (p-value < 0.001). The mean decay rates were 1.17 d -1 (95% CI: 1.06 to 1.27 d -1 ), 0.777 d -1 (0.716 to 0.838 d -1 ), and 0.450 d -1 (0.378 to 0.522 d -1 ) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies). Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95% to 99% reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95% and 99%, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95% and 99%, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome. We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation. In this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.
60 APPLIED LIFE SCIENCES↗
Nuclear Fuel Cycle Reasoner: PNNL FY12 Report
Building on previous internal investments and leveraging ongoing advancements in semantic technologies, PNNL implemented a formal reasoning framework and applied it to a specific challenge in nuclear nonproliferation. The Semantic Nonproliferation Analysis Platform (SNAP) was developed as a preliminary graphical user interface to demonstrate the potential power of the underlying semantic technologies to analyze and explore facts and relationships relating to the nuclear fuel cycle (NFC). In developing this proof of concept prototype, the utility and relevancy of semantic technologies to the Office of Defense Nuclear Nonproliferation Research and Development (DNN R&D) has been better understood.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
PANTHER. Pattern ANalytics To support High-performance Exploitation and Reasoning.
Sandia has approached the analysis of big datasets with an integrated methodology that uses computer science, image processing, and human factors to exploit critical patterns and relationships in large datasets despite the variety and rapidity of information. The work is part of a three-year LDRD Grand Challenge called PANTHER (Pattern ANalytics To support High-performance Exploitation and Reasoning). To maximize data analysis capability, Sandia pursued scientific advances across three key technical domains: (1) geospatial-temporal feature extraction via image segmentation and classification; (2) geospatial-temporal analysis capabilities tailored to identify and process new signatures more efficiently; and (3) domain- relevant models of human perception and cognition informing the design of analytic systems. Our integrated results include advances in geographical information systems (GIS) in which we discover activity patterns in noisy, spatial-temporal datasets using geospatial-temporal semantic graphs. We employed computational geometry and machine learning to allow us to extract and predict spatial-temporal patterns and outliers from large aircraft and maritime trajectory datasets. We automatically extracted static and ephemeral features from real, noisy synthetic aperture radar imagery for ingestion into a geospatial-temporal semantic graph. We worked with analysts and investigated analytic workflows to (1) determine how experiential knowledge evolves and is deployed in high-demand, high-throughput visual search workflows, and (2) better understand visual search performance and attention. Through PANTHER, Sandia's fundamental rethinking of key aspects of geospatial data analysis permits the extraction of much richer information from large amounts of data. The project results enable analysts to examine mountains of historical and current data that would otherwise go untouched, while also gaining meaningful, measurable, and defensible insights into overlooked relationships and patterns. The capability is directly relevant to the nation's nonproliferation remote-sensing activities and has broad national security applications for military and intelligence- gathering organizations.
58 GEOSCIENCES↗
Reasoning About Computing in the Post-Moore world [Slides]
We are facing new challenges due to technology shifts and evolving mission requirements. Meeting these challenges requires careful reasoning about hardware and our applications. This is important for decisions we’re making for our codes following ATDM and our decisions about future platforms.
97 MATHEMATICS AND COMPUTING↗
Intelligent Process Visualization through Nuclear Operation Process Modeling, Reasoning, and Object Detection from Field Videos (Final Report)
This report is a deliverable for the “Final Report” task of DOE NEET Project 19-16790, "Context-Aware Safety Information Display for Nuclear Field Workers." This project's overall goal is to test the hypothesis that integrating computer vision and process reasoning methods will enable proactive visualization of the safe operation and maintenance processes of Nuclear Power Plants (NPP) for field workers. Augmented Reality (AR) glasses adopting such proactive safety information visualization techniques can significantly increase personnel safety and reduce the NPP’s operating costs. The current practice of monitoring NPPs requires workers to switch between digital models, data, and physical workspaces in identifying relevant but potentially occluded objects and in assessing the risks of operation and maintenance processes. On the other hand, frequently changed field conditions require field workers to report to supervisors for real-time guidance. Such guidance is essential to ensure that changing conditions will not invalidate or endanger the work order and other ongoing processes that may jeopardize NPP operations. Additionally, incorrect recognition of equipment objects can result in communication errors and safety problems. AR techniques can assist engineers in viewing the physical workspaces with objects labeled with detailed operation procedures and safety reminders during field operations. The project team developed an “Intelligent Context-Aware Safety Information Display” (ICAD) for supporting Nuclear Power Plant (NPP) field workers in achieving safe and efficient execution of a series of operational tasks in uncertain and changing workspaces of an NPP. Before designing the ICAD-AR prototype, the project team synthesized NPP operational knowledge models through literature review studies, surveys, interviews with domain experts, and knowledge modeling. The project team conducted an extensive study of the operational procedures of various NPPs, and digital technologies that can support the safe and efficient execution of those procedures in different NPP operational contexts. This literature review helped the project team conduct surveys and interviews with nuclear engineers and field workers to identify three categories of information. The NPP knowledge modeling efforts reveal that the three categories of information identified have different levels of importance in a typical procedure of carrying out a series of tasks to achieve a specific NPP operation goal (e.g., shutdown, mode changes). These three categories of information include 1) Workspace dynamics – the changing spatial arrangements of workspaces, tools, protection equipment, and supporting materials, 2) Workflow prognostics – the dynamic dependencies between different parts of an NPP that functionally support and influence each other in terms of safety and efficiency, and 3) Hazards – objects and spaces that contain hazardous materials or physical conditions that can pose risks to workers or mechanical systems. The project team has profiled the importance levels of these categories of information into a knowledge model. This knowledge model specifies what types of information are more critical for a given task in a given workspace so that computers can automatically identify critical objects and sensors in a scene for delivering context-ware safety information to field workers through AR devices. Significant research development of this project results in technical research outcomes and a prototyping system that illustrates the technical feasibility of establishing an ICAD-AR system supporting the proactive safety information display for nuclear field workers. This final report summarizes the project team’s technological achievements in the past three years. Overall, the project team completed the development and integration of five techniques into a prototype ICAD Augmented Reality (ICAD-AR) system and demonstrated the developed system’s real-time execution in a mechanical room. The project team completed the analysis of using this prototype in other types of workspaces based on 3D image data and digital design models collected from two additional workspaces (a water treatment plant and a flow loop training facility). The integrated techniques include 1) Natural Language Processing (NLP) algorithms supporting the generation and updates of nuclear fieldwork process models based on text analysis of work packages and operation manuals; 2) sensor log analysis for predicting control actions in given sensor reading contexts; 3) computer vision algorithms for automatic localization and navigation of workers; 4) object detection algorithms for identifying task-related objects and correlated sensors for safety checking; 5) AR technique as a platform for supporting the integration. The testing results of these five techniques have shown that 1) the sensor log analysis model can predict the next control action with an accuracy of 0.883; 2) the trained natural language processing model can extract more than 80% of the critical information from paper-based procedures (PBPs); 3) the navigation algorithm with the integration of Visual Inertial Odometry (VIO) and Non-Recursive Bayesian Filter methods make operator’s trajectory estimation resilient to drift error; 4) the computer vision algorithm can detect task-specific and safety-critical objects with an average accuracy of 95.3%. The project team used work procedures collected from a flow loop training facility and two datasets collected from two mechanical rooms simulating the workspaces of NPPs to demonstrate the technical capabilities of the developed ICAD-AR prototype. The demonstration validated the technical feasibility of establishing the ICAD-AR system for nuclear field workers and identified the challenges in 1) automatic text analysis of work packages; 2) use of limited samples of sensor logs for predicting the proper timings of control actions; 3) reliably tracking workers and their task progress in mechanical rooms with many similar objects.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Reasons for yearly variation of the atmospheric electric field potential gradient
Reasons for yearly variation of atmospheric electric field potential gradient
POTENTIAL GRADIENT↗
Reasoning by analogy as an aid to heuristic theorem proving.
When heuristic problem-solving programs are faced with large data bases that contain numbers of facts far in excess of those needed to solve any particular problem, their performance rapidly deteriorates. In this paper, the correspondence between a new unsolved problem and a previously solved analogous problem is computed and invoked to tailor large data bases to manageable sizes. This paper outlines the design of an algorithm for generating and exploiting analogies between theorems posed to a resolution-logic system. These algorithms are believed to be the first computationally feasible development of reasoning by analogy to be applied to heuristic theorem proving.
Kling, R. E.↗
Reasons for low aerodynamic performance of 13.5-centimeter-tip-diameter aircraft engine starter turbine
The reasons for the low aerodynamic performance of a 13.5 cm tip diameter aircraft engine starter turbine were investigated. Both the stator and the stage were evaluated. Approximately 10 percent improvement in turbine efficiency was obtained when the honeycomb shroud over the rotor blade tips was filled to obtain a solid shroud surface. Efficiency improvements were obtained for three rotor configurations when the shroud was filled. It is suggested that the large loss associated with the open honeycomb shroud is due primarily to energy loss associated with gas transportation as a result of the blade to blade pressure differential at the tip section.
Haas, J. E.↗
Spatial reasoning to determine stream network from LANDSAT imagery
In LANDSAT imagery, spectral and spatial information can be used to detect the drainage network as well as the relative elevation model in mountainous terrain. To do this, mixed information of material reflectance in the original LANDSAT imagery must be separated. From the material reflectance information, big visible rivers can be detected. From the topographic modulation information, ridges and valleys can be detected and assigned relative elevations. A complete elevation model can be generated by interpolating values for nonridge and non-valley pixels. The small streams not detectable from material reflectance information can be located in the valleys with flow direction known from the elevation model. Finally, the flow directions of big visible rivers can be inferred by solving a consistent labeling problem based on a set of spatial reasoning constraints.
Haralick, R. M.↗
Geological reasons for change in intensity of linear magnetic anomalies of the Kursk magnetic anomaly
The geological reasons for fluctuations in the anomalous field intensity along the polar axes were examined. The Kursk magnetic anomaly is used as the basis for the study. A geological-geophysical section was constructed which used the results of the interpretation of gravimagnetic anomalies.
Zhavoronkin, I. A.↗
Six reasons why thermospheric measurements and models disagree
The differences between thermospheric measurements and models are discussed. Sometimes the model is in error and at other times the measurements are, but it also is possible for both to be correct, yet have the comparison result in an apparent disagreement. These reasons are collected for disagreement, and, whenever possible, methods of reducing or eliminating them are suggested. The six causes of disagreement discussed are: actual errors caused by the limited knowledge of gas-surface interactions and by in-track winds; limitations of the thermospheric general circulation models due to incomplete knowledge of the energy sources and sinks as well as incompleteness of the parameterization which must be employed; and limitations imposed on the empirical models by the conceptual framework and the transient waves.
Moe, Kenneth↗
An efficient representation of spatial information for expert reasoning in robotic vehicles
The previous generation of robotic vehicles and drones was designed for a specific task, with limited flexibility in executing their mission. This limited flexibility arises because the robotic vehicles do not possess the intelligence and knowledge upon which to make significant tactical decisions. Current development of robotic vehicles is toward increased intelligence and capabilities, adapting to a changing environment and altering mission objectives. The latest techniques in artificial intelligence (AI) are being employed to increase the robotic vehicle's intelligent decision-making capabilities. This document describes the design of the SARA spatial database tool, which is composed of request parser, reasoning, computations, and database modules that collectively manage and derive information useful for robotic vehicles.
Scott, Steven↗
PDA: A coupling of knowledge and memory for case-based reasoning
Problem solving in most domains requires reference to past knowledge and experience whether such knowledge is represented as rules, decision trees, networks or any variant of attributed graphs. Regardless of the representational form employed, designers of expert systems rarely make a distinction between the static and dynamic aspects of the system's knowledge base. The current paper clearly distinguishes between knowledge-based and memory-based reasoning where the former in its most pure sense is characterized by a static knowledge based resulting in a relatively brittle expert system while the latter is dynamic and analogous to the functions of human memory which learns from experience. The paper discusses the design of an advisory system which combines a knowledge base consisting of domain vocabulary and default dependencies between concepts with a dynamic conceptual memory which stores experimental knowledge in the form of cases. The case memory organizes past experience in the form of MOPs (memory organization packets) and sub-MOPs. Each MOP consists of a context frame and a set of indices. The context frame contains information about the features (norms) common to all the events and sub-MOPs indexed under it.
Bharwani, S.↗
Simple explanations and reasoning: From philosophy of science to expert systems
A preliminary prototype of a simple explanation system was constructed. Although the system, based on the idea of storytelling, did not incorporate all of the principles of simple explanation, it did demonstrate the potential of the approach. The system incorporated a hypertext system, an inference engine, and facilities for constructing contrast type explanations. The continued development of such a system should prove to be valuable. By extending the resources of the expert system paradigm, the knowledge engineer is not forced to learn a new set of skills, and the domain knowledge already acquired by him is not lost. Further, both the beginning user and the more advanced user can be accommodated. For the beginning user, corrective explanations and ES explanations provide facilities for more clearly understanding the way in which the system is functioning. For the more advanced user, the instance and state explanations allow him to focus on the issues at hand. The simple model of explanation attempts to exploit and show how the why and how facilities of the expert system paradigm can be extended by attending to the pragmatics of explanation and adding texture to the ordinary pattern of reasoning in a rule based system.
Rochowiak, Daniel↗
Geometric reasoning
Cognitive robot systems are ones in which sensing and representation occur, from which task plans and tactics are determined. Such a robot system accomplishes a task after being told what to do, but determines for itself how to do it. Cognition is required when the work environment is uncontrolled, when contingencies are prevalent, or when task complexity is large; it is useful in any robotic mission. A number of distinguishing features can be associated with cognitive robotics, and one emphasized here is the role of artificial intelligence in knowledge representation and in planning. While space telerobotics may elude some of the problems driving cognitive robotics, it shares many of the same demands, and it can be assumed that capabilities developed for cognitive robotics can be employed advantageously for telerobotics in general. The top level problem is task planning, and it is appropriate to introduce a hierarchical view of control. Presented with certain mission objectives, the system must generate plans (typically) at the strategic, tactical, and reflexive levels. The structure by which knowledge is used to construct and update these plans endows the system with its cognitive attributes, and with the ability to deal with contingencies, changes, unknowns, and so on. Issues of representation and reasoning which are absolutely fundamental to robot manipulation, decisions based upon geometry, are discussed here, not AI task planning per se.
Woodbury, R. F.↗