Dataset Information

A unified model of human semantic knowledge and its disorders.

ABSTRACT: How is knowledge about the meanings of words and objects represented in the human brain? Current theories embrace two radically different proposals: either distinct cortical systems have evolved to represent different kinds of things, or knowledge for all kinds is encoded within a single domain-general network. Neither view explains the full scope of relevant evidence from neuroimaging and neuropsychology. Here we propose that graded category-specificity emerges in some components of the semantic network through joint effects of learning and network connectivity. We test the proposal by measuring connectivity amongst cortical regions implicated in semantic representation, then simulating healthy and disordered semantic processing in a deep neural network whose architecture mirrors this structure. The resulting neuro-computational model explains the full complement of neuroimaging and patient evidence adduced in support of both domain-specific and domain-general approaches, reconciling long-standing disputes about the nature and origins of this uniquely human cognitive faculty.

SUBMITTER: Chen L

PROVIDER: S-EPMC5417358 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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A unified model of human semantic knowledge and its disorders.

Chen Lang L Lambon Ralph Matthew A MA Rogers Timothy T TT

Nature human behaviour 20170301 3

How is knowledge about the meanings of words and objects represented in the human brain? Current theories embrace two radically different proposals: either distinct cortical systems have evolved to represent different kinds of things, or knowledge for all kinds is encoded within a single domain-general network. Neither view explains the full scope of relevant evidence from neuroimaging and neuropsychology. Here we propose that graded category-specificity emerges in some components of the semanti ...[more]

PMID: 28480333

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Project description:BACKGROUND:Over the past several centuries, chemistry has permeated virtually every facet of human lifestyle, enriching fields as diverse as medicine, agriculture, manufacturing, warfare, and electronics, among numerous others. Unfortunately, application-specific, incompatible chemical information formats and representation strategies have emerged as a result of such diverse adoption of chemistry. Although a number of efforts have been dedicated to unifying the computational representation of chemical information, disparities between the various chemical databases still persist and stand in the way of cross-domain, interdisciplinary investigations. Through a common syntax and formal semantics, Semantic Web technology offers the ability to accurately represent, integrate, reason about and query across diverse chemical information. RESULTS:Here we specify and implement the Chemical Entity Semantic Specification (CHESS) for the representation of polyatomic chemical entities, their substructures, bonds, atoms, and reactions using Semantic Web technologies. CHESS provides means to capture aspects of their corresponding chemical descriptors, connectivity, functional composition, and geometric structure while specifying mechanisms for data provenance. We demonstrate that using our readily extensible specification, it is possible to efficiently integrate multiple disparate chemical data sources, while retaining appropriate correspondence of chemical descriptors, with very little additional effort. We demonstrate the impact of some of our representational decisions on the performance of chemically-aware knowledgebase searching and rudimentary reaction candidate selection. Finally, we provide access to the tools necessary to carry out chemical entity encoding in CHESS, along with a sample knowledgebase. CONCLUSIONS:By harnessing the power of Semantic Web technologies with CHESS, it is possible to provide a means of facile cross-domain chemical knowledge integration with full preservation of data correspondence and provenance. Our representation builds on existing cheminformatics technologies and, by the virtue of RDF specification, remains flexible and amenable to application- and domain-specific annotations without compromising chemical data integration. We conclude that the adoption of a consistent and semantically-enabled chemical specification is imperative for surviving the coming chemical data deluge and supporting systems science research.

Project description:OBJECTIVE:Phenotyping algorithms can efficiently and accurately identify patients with a specific disease phenotype and construct electronic health records (EHR)-based cohorts for subsequent clinical or genomic studies. Previous studies have introduced unsupervised EHR-based feature selection methods that yielded algorithms with high accuracy. However, those selection methods still require expert intervention to tweak the parameter settings according to the EHR data distribution for each phenotype. To further accelerate the development of phenotyping algorithms, we propose a fully automated and robust unsupervised feature selection method that leverages only publicly available medical knowledge sources, instead of EHR data. METHODS:SEmantics-Driven Feature Extraction (SEDFE) collects medical concepts from online knowledge sources as candidate features and gives them vector-form distributional semantic representations derived with neural word embedding and the Unified Medical Language System Metathesaurus. A number of features that are semantically closest and that sufficiently characterize the target phenotype are determined by a linear decomposition criterion and are selected for the final classification algorithm. RESULTS:SEDFE was compared with the EHR-based SAFE algorithm and domain experts on feature selection for the classification of five phenotypes including coronary artery disease, rheumatoid arthritis, Crohn's disease, ulcerative colitis, and pediatric pulmonary arterial hypertension using both supervised and unsupervised approaches. Algorithms yielded by SEDFE achieved comparable accuracy to those yielded by SAFE and expert-curated features. SEDFE is also robust to the input semantic vectors. CONCLUSION:SEDFE attains satisfying performance in unsupervised feature selection for EHR phenotyping. Both fully automated and EHR-independent, this method promises efficiency and accuracy in developing algorithms for high-throughput phenotyping.

Dataset Information

A unified model of human semantic knowledge and its disorders.

Publications

A unified model of human semantic knowledge and its disorders.

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