Unified Semantics Research Articles

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.

Accounting for counting: A unified semantics for measure terms and classifiers

This paper develops and extends the semantic account of morphological number marking in the presence of numerals from Scontras (2013). The account handles variation in patterns of number marking along two dimensions: cross-linguistically, between languages that either necessitate or prohibit singular morphology in the presence of numerals greater than ‘one’, and within one and the same language: English. The proposed semantics accounts for both sorts of variation by assuming flexibility in the selection of the measure relevant to the one-ness presupposition of the morphological singular form. The system also provides an explanation for the Slobin-Greenberg-Sanches Generalization, which states that no classifier language has obligatory number marking: by aligning the semantics of counting in both number marking and classifier languages, and by assuming that nouns in classifier languages denote kinds, the semantic contribution of number marking is necessarily redundant in classifier languages. A system of obligatory number marking only surfaces in languages where it delivers otherwise unrecoverable information about the number of intended referents.

What do quantifier particles do?

In many languages, the same particles that form quantifier words also serve as connectives, additive and scalar particles, question markers, roots of existential verbs, and so on. Do these have a unified semantics, or do they merely bear a family resemblance? Are they aided by silent operators in their varied roles―if yes, what operators? I dub the particles “quantifier particles” and refer to them generically with capitalized versions of the Japanese morphemes. I argue that both MO and KA can be assigned a stable semantics across their various roles. The specific analysis I offer is motivated by the fact that MO and KA often combine with just one argument; I propose that this is their characteristic behavior. Their role is to impose semantic requirements that are satisfied when the immediately larger context is interpreted as the meet/join of their host’s semantic contribution with something else. They do not perform meet/join themselves. The obligatory vs. optional appearance of the particles depends on whether the meet/join interpretations arise by default in the given constellation. I explicate the proposal using the toolkit of basic Inquisitive Semantics.

The Neural Mechanism and Influential Factors of Semantic Unification in Discourse Comprehension

The Neural Mechanism and Influential Factors of Semantic Unification in Discourse Comprehension

Towards maximal unification of semantically diverse ontologies for controversial domains

Purpose – Ontologies are prone to wide semantic variability due to subjective points of view of their composers. The purpose of this paper is to propose a new approach for maximal unification of diverse ontologies for controversial domains by their relations. Design/methodology/approach – Effective matching or unification of multiple ontologies for a specific domain is crucial for the success of many semantic web applications, such as semantic information retrieval and organization, document tagging, summarization and search. To this end, numerous automatic and semi-automatic techniques were proposed in the past decade that attempt to identify similar entities, mostly classes, in diverse ontologies for similar domains. Apparently, matching individual entities cannot result in full integration of ontologies’ semantics without matching their inter-relations with all other-related classes (and instances). However, semantic matching of ontological relations still constitutes a major research challenge. Therefore, in this paper the authors propose a new paradigm for assessment of maximal possible matching and unification of ontological relations. To this end, several unification rules for ontological relations were devised based on ontological reference rules, and lexical and textual entailment. These rules were semi-automatically implemented to extend a given ontology with semantically matching relations from another ontology for a similar domain. Then, the ontologies were unified through these similar pairs of relations. The authors observe that these rules can be also facilitated to reveal the contradictory relations in different ontologies. Findings – To assess the feasibility of the approach two experiments were conducted with different sets of multiple personal ontologies on controversial domains constructed by trained subjects. The results for about 50 distinct ontology pairs demonstrate a good potential of the methodology for increasing inter-ontology agreement. Furthermore, the authors show that the presented methodology can lead to a complete unification of multiple semantically heterogeneous ontologies. Research limitations/implications – This is a conceptual study that presents a new approach for semantic unification of ontologies by a devised set of rules along with the initial experimental evidence of its feasibility and effectiveness. However, this methodology has to be fully automatically implemented and tested on a larger dataset in future research. Practical implications – This result has implication for semantic search, since a richer ontology, comprised of multiple aspects and viewpoints of the domain of knowledge, enhances discoverability and improves search results. Originality/value – To the best of the knowledge, this is the first study to examine and assess the maximal level of semantic relation-based ontology unification.

The neurobiology of language beyond single words.

A hallmark of human language is that we combine lexical building blocks retrieved from memory in endless new ways. This combinatorial aspect of language is referred to as unification. Here we focus on the neurobiological infrastructure for syntactic and semantic unification. Unification is characterized by a high-speed temporal profile including both prediction and integration of retrieved lexical elements. A meta-analysis of numerous neuroimaging studies reveals a clear dorsal/ventral gradient in both left inferior frontal cortex and left posterior temporal cortex, with dorsal foci for syntactic processing and ventral foci for semantic processing. In addition to core areas for unification, further networks need to be recruited to realize language-driven communication to its full extent. One example is the theory of mind network, which allows listeners and readers to infer the intended message (speaker meaning) from the coded meaning of the linguistic utterance. This indicates that sensorimotor simulation cannot handle all of language processing.

Against Logically Possible World-Relativized Existence

Abstract The thesis that entities exist in, at, or in relation to logically possible worlds is criticized. The suggestion that actually nonexistent fictional characters might nevertheless exist in nonactual merely logically possible worlds runs afoul of the most general transworld identity requirements. An influential philosophical argument for the concept of world-relativized existence is examined in Alvin Plantinga’s formal development and explanation of modal semantic relations. Despite proposing an attractive unified semantics of alethic modality, Plantinga’s argument is rejected on formal grounds as supporting materially false actual existence assertions in the case of actually nonexistent objects in the framework of Plantinga’s own underlying classical predicate-quantificational logic.

The construction of viewpoint aspect: the imperfective revisited

This paper argues for a constructionist approach to viewpoint Aspect by exploring the idea that it does not exert any altering force on the situation-aspect properties of predicates. The proposal is developed by analyzing the syntax and semantics of the imperfective, which has been attributed a coercer role in the literature as a de-telicizer and de-stativizer in the progressive, and as a de-eventivizer in the so-called ability (or attitudinal) and habitual readings. This paper proposes a unified semantics for the imperfective, preserving the properties of eventualities throughout the derivation. The paper argues that the semantics of viewpoint aspect is encoded in a series of functional heads containing interval-ordering predicates and quantifiers. This richer structure allows us to account for a greater amount of phenomena, such as the perfective nature of the individual instantiations of the event within a habitual construction or the nonculminating reading of perfective accomplishments in Spanish. This paper hypothesizes that nonculminating accomplishments have an underlying structure corresponding to the perfective progressive. As a consequence, the progressive becomes disentangled from imperfectivity and is given a novel analysis. The proposed syntax is argued to have a corresponding explicit morphology in languages such as Spanish and a nondifferentiating one in languages such as English; however, the syntax-semantics underlying both of these languages is argued to be the same.

Accounting for counting: A unified semantics for measure terms and classifiers

This paper develops and extends the semantic account of morphological number marking in the presence of numerals from Scontras (2013). The account handles variation in patterns of number marking along two dimensions: cross-linguistically, between languages that either necessitate or prohibit singular morphology in the presence of numerals greater than ‘one’, and within one and the same language: English. The proposed semantics accounts for both sorts of variation by assuming flexibility in the selection of the measure relevant to the one-ness presupposition of the morphological singular form. The system also provides an explanation for the Slobin-Greenberg-Sanches Generalization, which states that no classifier language has obligatory number marking: by aligning the semantics of counting in both number marking and classifier languages, and by assuming that nouns in classifier languages denote kinds, the semantic contribution of number marking is necessarily redundant in classifier languages. A system of obligatory number marking only surfaces in languages where it delivers otherwise unrecoverable information about the number of intended referents.

Revisioning the unification of syntax, semantics and statistics in shape analysis

Hidden patterns, rendered visible by hindsight, often stand revealed as strong influences. Rama Chellappa’s lab in the mid to late ’80s molded our character and scholarship in more ways than one. Rama ably handled the transition from image processing to computer vision and established an applied math and computing infrastructure from which we continue to benefit. In particular, the themes important to King-Sun Fu—syntax, semantics and statistics—were all debated in Rama’s lab at that time. We argue that this triad remains important. With syntactic representations losing mindshare to statistics, we remain in the hunt for unification. And with the syntax versus semantics debate unresolved, it deserves a hearing as well. We offer two themes—uncertainty and interaction—to aid in the process of unification. First, we show that complex wave functions carry probabilistic location information in their magnitude and syntactic (curve) information in their phase while representing uncertainty at a fundamental level. Next, after reviewing work in analytic philosophy, we connect semantics to intentional, mental content. Analytic philosophy reminds us to take human experience seriously but remaining physicalist if possible. To this end, we introduce a nondualist interactionist model of experience, wherein compositional (physical) subjects are constantly shaping and being shaped by a physical world. We then demonstrate that wave functions can accommodate interaction, closely tracking previous work in physics on the measurement problem. The linearity and superposition properties of wave functions allow for literal addition of waves created by human interaction with shapes. Finally, we briefly survey the current situation in the human–computer interaction (HCI) field and argue that mathematical models of interaction akin to those in pattern recognition can aid HCI. We close by arguing that we can follow in Fu’s footsteps and incorporate the mathematical modeling of human interaction into pattern recognition.

A Semantic Approach for Automatic Structuring and Analysis of Software Process Patterns

The main contribution of this paper, is to propose a novel semantic approach based on a Natural Language Processing technique in order to ensure a semantic unification of unstructured process patterns which are expressed not only in different formats but also, in different forms. This approach is implemented using the GATE text engineering framework and then evaluated leading up to high-quality results motivating us to continue in this direction.

Extended designs algebraically

Extended designs distinguish non-terminating and aborting executions of sequential, non-deterministic programs. We show how to treat them algebraically based on techniques we have previously applied to total and general correctness approaches. In particular, we propose modifications to the definition of an extended design which make the theory more clear and simplify calculations, and an approximation order for recursion. We derive explicit formulas for operators on extended designs including non-deterministic choice, sequential composition, while-loops and full recursion. We show how to represent extended designs as designs or prescriptions over an extended state space. The new theory generalises our previous algebraic theory of general correctness by weakening its axioms. It also integrates with partial, total and general correctness into a common foundation which gives a unified semantics of while-programs. Program transformations derived using this semantics are valid in all four correctness approaches.

Neural correlates of combinatorial semantic processing of literal and figurative noun noun compound words

The right hemisphere's role in language comprehension is supported by results from several neuropsychology and neuroimaging studies. Special interest surrounds right temporoparietal structures, which are thought to be involved in processing novel metaphorical expressions, primarily due to the coarse semantic coding of concepts. In this event related fMRI experiment we aimed at assessing the extent of semantic distance processing in the comprehension of figurative meaning to clarify the role of the right hemisphere. Four categories of German noun noun compound words were presented in a semantic decision task: a) conventional metaphors; b) novel metaphors; c) conventional literal, and; d) novel literal expressions, controlled for length, frequency, imageability, arousal, and emotional valence. Conventional literal and metaphorical compounds increased BOLD signal change in right temporoparietal regions, suggesting combinatorial semantic processing, in line with the coarse semantic coding theory, but at odds with the graded salience hypothesis. Both novel literal and novel metaphorical expressions increased activity in left inferior frontal areas, presumably as a result of phonetic, morphosyntactic, and semantic unification processes, challenging predictions regarding right hemispheric involvement in processing unusual meanings. Meanwhile, both conventional and novel metaphorical expressions induced BOLD signal change in left hemispherical regions, suggesting that even novel metaphor processing involves more than linking semantically distant concepts.

Beta oscillations relate to the N400m during language comprehension

The relationship between the evoked responses (ERPs/ERFs) and the event-related changes in EEG/MEG power that can be observed during sentence-level language comprehension is as yet unclear. This study addresses a possible relationship between MEG power changes and the N400m component of the event-related field. Whole-head MEG was recorded while subjects listened to spoken sentences with incongruent (IC) or congruent (C) sentence endings. A clear N400m was observed over the left hemisphere, and was larger for the IC sentences than for the C sentences. A time-frequency analysis of power revealed a decrease in alpha and beta power over the left hemisphere in roughly the same time range as the N400m for the IC relative to the C condition. A linear regression analysis revealed a positive linear relationship between N400m and beta power for the IC condition, not for the C condition. No such linear relation was found between N400m and alpha power for either condition. The sources of the beta decrease were estimated in the LIFG, a region known to be involved in semantic unification operations. One source of the N400m was estimated in the left superior temporal region, which has been related to lexical retrieval. We interpret our data within a framework in which beta oscillations are inversely related to the engagement of task-relevant brain networks. The source reconstructions of the beta power suppression and the N400m effect support the notion of a dynamic communication between the LIFG and the left superior temporal region during language comprehension.

Understanding counterfactuals in discourse modulates ERP and oscillatory gamma rhythms in the EEG

This study provides ERP and oscillatory dynamics data associated with the comprehension of narratives involving counterfactual events. Participants were given short stories describing an initial situation (“Marta wanted to plant flowers in her garden….”), followed by a critical sentence describing a new situation in either a factual (“Since she found a spade, she started to dig a hole”) or counterfactual format (“If she had found a spade, she would have started to dig a hole”), and then a continuation sentence that was either related to the initial situation (“she bought a spade”) or to the new one (“she planted roses”). The ERPs recorded for the continuation sentences related to the initial situation showed larger negativity after factuals than after counterfactuals, suggesting that the counterfactual's presupposition – the events did not occur – prevents updating the here-and-now of discourse. By contrast, continuation sentences related to the new situation elicited similar ERPs under both factual and counterfactual contexts, suggesting that counterfactuals also activate momentarily an alternative “as if” meaning. However, the reduction of gamma power following counterfactuals, suggests that the “as if” meaning is not integrated into the discourse, nor does it contribute to semantic unification processes.

Modeling of complex systems II: A minimalist and unified semantics for heterogeneous integrated systems

The purpose of this paper is to contribute to a unified formal framework for complex systems modeling. To this aim, we define a unified semantics for systems including integration operators. We consider complex systems as functional blackboxes (with internal states), whose structure and behaviors can be constructed through a recursive integration of heterogeneous components. We first introduce formal definitions of time (allowing to deal uniformly with both continuous and discrete times) and data (allowing to handle heterogeneous data), and introduce a generic synchronization mechanism for dataflows. We then define a system as a mathematical object characterized by coupled functional and states behaviors. This definition is expressive enough to capture the functional behavior of any real system with sequential transitions. We finally provide formal operators for integrating systems and show that they are consistent with the classical definitions of those operators on transfer functions which model real systems.

The anterior left inferior frontal gyrus contributes to semantic unification

Semantic unification, the process by which small blocks of semantic information are combined into a coherent utterance, has been studied with various types of tasks. However, whether the brain activations reported in these studies are attributed to semantic unification per se or to other task-induced concomitant processes still remains unclear. The neural basis for semantic unification in sentence comprehension was examined using event-related potentials (ERP) and functional Magnetic Resonance Imaging (fMRI). The semantic unification load was manipulated by varying the goodness of fit between a critical word and its preceding context (in high cloze, low cloze and violation sentences). The sentences were presented in a serial visual presentation mode. The participants were asked to perform one of three tasks: semantic congruency judgment (SEM), silent reading for comprehension (READ), or font size judgment (FONT), in separate sessions. The ERP results showed a similar N400 amplitude modulation by the semantic unification load across all of the three tasks. The brain activations associated with the semantic unification load were found in the anterior left inferior frontal gyrus (aLIFG) in the FONT task and in a widespread set of regions in the other two tasks. These results suggest that the aLIFG activation reflects a semantic unification, which is different from other brain activations that may reflect task-specific strategic processing.

Towards Agile Application Integration with M2M Platforms

M2M (Machine-to-Machine) Technology makes it possible to network all kinds of terminal devices and their corresponding enterprise applications. Therefore, several M2M platforms were developed in China in order to collect information from terminal devices dispersed all over the local places through 3G wireless network. However, when enterprise applications try to integrate with M2M platforms, they should be maintained and refactored to adapt the heterogeneous features and properties of M2M platforms. Moreover, syntactical and semantic unification for information sharing among applications and devices are still unsolved because of raw data transmission and the usage of distinguished business vocabularies. In this paper, we propose and develop an M2M Middleware to support agile application integration with M2M platform. This middleware imports the event engine and XML-based syntax to handle the syntactical unification, makes use of Ontology-based semantic mapping to solve the semantic unification and adopts WebService and ETL techniques to sustain multi-pattern interactive approach, in order to agilely make applications integrated with the M2M platform. Now, the M2M Middleware has been applied in the China Telecom M2M platform. The operation results show that applications will cost less time and workload when being integrated with M2M platform.

Integration or Predictability? A Further Specification of the Functional Role of Gamma Oscillations in Language Comprehension

Gamma-band neuronal synchronization during sentence-level language comprehension has previously been linked with semantic unification. Here, we attempt to further narrow down the functional significance of gamma during language comprehension, by distinguishing between two aspects of semantic unification: successful integration of word meaning into the sentence context, and prediction of upcoming words. We computed event-related potentials (ERPs) and frequency band-specific electroencephalographic (EEG) power changes while participants read sentences that contained a critical word (CW) that was (1) both semantically congruent and predictable (high cloze, HC), (2) semantically congruent but unpredictable (low cloze, LC), or (3) semantically incongruent (and therefore also unpredictable; semantic violation, SV). The ERP analysis showed the expected parametric N400 modulation (HC < LC < SV). The time-frequency analysis showed qualitatively different results. In the gamma-frequency range, we observed a power increase in response to the CW in the HC condition, but not in the LC and the SV conditions. Additionally, in the theta frequency range we observed a power increase in the SV condition only. Our data provide evidence that gamma power increases are related to the predictability of an upcoming word based on the preceding sentence context, rather than to the integration of the incoming word’s semantics into the preceding context. Further, our theta band data are compatible with the notion that theta band synchronization in sentence comprehension might be related to the detection of an error in the language input.

Institutionalising UML 2.0 state machines

A key challenge to achieve a unified semantics for UML is how to handle the heterogeneity of its sublanguages. In this context, the theory of institutions provides an elegant and robust framework for programming in the large and in particular for compositionality. It can be used to define a family of formalisms which capture various UML sublanguages, and morphisms that represent the expected semantic relationships between them, resulting in a heterogeneous environment for the semantic definition of UML. The main goal of this work is to collaborate with the definition of such environment. For this purpose, we define an institution for UML 2.0 state machines. The building blocks of our institution are based on a previous semantics dealing with processing simple input events within a transition step. We also extend these semantic definitions for handling sequences of events, and then for considering runs through the state machine.