Humans depart from optimal computational models of interactive decision-making during competition under partial information.

Decision making under uncertainty in multiagent settings is of increasing interest in decision science. The degree to which human agents depart from computationally optimal solutions in socially interactive settings is generally unknown. Such understanding provides insight into how social contexts affect human interaction and the underlying contributions of Theory of Mind. In this paper, we adapt the well-known 'Tiger Problem' from artificial-agent research to human participants in solo and interactive settings. Compared to computationally optimal solutions, participants gathered less information before outcome-related decisions when competing than cooperating with others. These departures from optimality were not haphazard but showed evidence of improved performance through learning. Costly errors emerged under conditions of competition, yielding both lower rates of rewarding actions and accuracy in predicting others. Taken together, this work provides a novel approach and insights into studying human social interaction when shared information is partial.

Theory of mind and decision science: Towards a typology of tasks and computational models.

The ability to form a Theory of Mind (ToM), i.e., to theorize about others' mental states to explain and predict behavior in relation to attributed intentional states, constitutes a hallmark of human cognition. These abilities are multi-faceted and include a variety of different cognitive sub-functions. Here, we focus on decision processes in social contexts and review a number of experimental and computational modeling approaches in this field. We provide an overview of experimental accounts and formal computational models with respect to two dimensions: interactivity and uncertainty. Thereby, we aim at capturing the nuances of ToM functions in the context of social decision processes. We suggest there to be an increase in ToM engagement and multiplexing as social cognitive decision-making tasks become more interactive and uncertain. We propose that representing others as intentional and goal directed agents who perform consequential actions is elicited only at the edges of these two dimensions. Further, we argue that computational models of valuation and beliefs follow these dimensions to best allow researchers to effectively model sophisticated ToM-processes. Finally, we relate this typology to neuroimaging findings in neurotypical (NT) humans, studies of persons with autism spectrum (AS), and studies of nonhuman primates.

A framework for ontology-based question answering with application to parasite immunology.

BACKGROUND: Large quantities of biomedical data are being produced at a rapid pace for a variety of organisms. With ontologies proliferating, data is increasingly being stored using the RDF data model and queried using RDF based querying languages. While existing systems facilitate the querying in various ways, the scientist must map the question in his or her mind to the interface used by the systems. The field of natural language processing has long investigated the challenges of designing natural language based retrieval systems. Recent efforts seek to bring the ability to pose natural language questions to RDF data querying systems while leveraging the associated ontologies. These analyze the input question and extract triples (subject, relationship, object), if possible, mapping them to RDF triples in the data. However, in the biomedical context, relationships between entities are not always explicit in the question and these are often complex involving many intermediate concepts. RESULTS: We present a new framework, OntoNLQA, for querying RDF data annotated using ontologies which allows posing questions in natural language. OntoNLQA offers five steps in order to answer natural language questions. In comparison to previous systems, OntoNLQA differs in how some of the methods are realized. In particular, it introduces a novel approach for discovering the sophisticated semantic associations that may exist between the key terms of a natural language question, in order to build an intuitive query and retrieve precise answers. We apply this framework to the context of parasite immunology data, leading to a system called AskCuebee that allows parasitologists to pose genomic, proteomic and pathway questions in natural language related to the parasite, Trypanosoma cruzi. We separately evaluate the accuracy of each component of OntoNLQA as implemented in AskCuebee and the accuracy of the whole system. AskCuebee answers 68 % of the questions in a corpus of 125 questions, and 60 % of the questions in a new previously unseen corpus. If we allow simple corrections by the scientists, this proportion increases to 92 %. CONCLUSIONS: We introduce a novel framework for question answering and apply it to parasite immunology data. Evaluations of translating the questions to RDF triple queries by combining machine learning, lexical similarity matching with ontology classes, properties and instances for specificity, and discovering associations between them demonstrate that the approach performs well and improves on previous systems. Subsequently, OntoNLQA offers a viable framework for building question answering systems in other biomedical domains.

Speeding up Batch Alignment of Large Ontologies Using MapReduce.

Real-world ontologies tend to be very large with several containing thousands of entities. Increasingly, ontologies are hosted in repositories, which often compute the alignment between the ontologies. As new ontologies are submitted or ontologies are updated, their alignment with others must be quickly computed. Therefore, aligning several pairs of ontologies quickly becomes a challenge for these repositories. We project this problem as one of batch alignment and show how it may be approached using the distributed computing paradigm of MapReduce. Our approach allows any alignment algorithm to be utilized on a MapReduce architecture. Experiments using four representative alignment algorithms demonstrate flexible and significant speedup of batch alignment of large ontology pairs using MapReduce.

A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi.

BACKGROUND: Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge. METHODOLOGY/PRINCIPAL FINDINGS: We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results. CONCLUSION/SIGNIFICANCE: The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.

Inexact Matching of Ontology Graphs Using Expectation-Maximization.

We present a new method for mapping ontology schemas that address similar domains. The problem of ontology matching is crucial since we are witnessing a decentralized development and publication of ontological data. We formulate the problem of inferring a match between two ontologies as a maximum likelihood problem, and solve it using the technique of expectation-maximization (EM). Specifically, we adopt directed graphs as our model for ontology schemas and use a generalized version of EM to arrive at a map between the nodes of the graphs. We exploit the structural, lexical and instance similarity between the graphs, and differ from the previous approaches in the way we utilize them to arrive at, a possibly inexact, match. Inexact matching is the process of finding a best possible match between the two graphs when exact matching is not possible or is computationally difficult. In order to scale the method to large ontologies, we identify the computational bottlenecks and adapt the generalized EM by using a memory bounded partitioning scheme. We provide comparative experimental results in support of our method on two well-known ontology alignment benchmarks and discuss their implications.

Time to laparotomy for intra-abdominal bleeding from trauma does affect survival for delays up to 90 minutes.

OBJECTIVE: We examined the relationship between survival and time in the emergency department (ED) before laparotomy for hypotensive patients bleeding from abdominal injuries. METHODS: Patients in the Pennsylvania Trauma Systems Foundation trauma registry with isolated abdominal vascular, solid organ, or wall injuries grade 3 to 6 and hypotension were identified. Deaths were predicted from the prehospital time, systolic blood pressure (SBP) on ED admission, and time in the ED before either laparotomy or ED death. RESULTS: Two-hundred forty-three patients met the criteria. SBP ranged from 30 to 90 mm Hg. Time to the ED ranged from 7 to 185 minutes. Time in the ED ranged from 7 to 915 minutes. Overall, 98 patients died (40%). The risk ratio for the SBP increased, as expected, as SBP dropped. The risk ratio for time spent in the ED before laparotomy increased until 90 minutes, then significantly decreased below all earlier values. Logistic regression on the 165 patients spending 90 minutes or less in the ED showed that the probability of death increased with time in the ED. The increase was as much as 0.35% per minute. CONCLUSION: Among patients in a trauma registry who were hypotensive on arrival in the ED and had major injuries isolated to the abdomen requiring emergency laparotomy, the probability of death showed a relationship to both the extent of hypotension and the length of time in the ED for patients who were in the ED for 90 minutes or less. The probability of death increased approximately 1% for each 3 minutes in the ED.