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BMC Bioinformatics Oct 2020Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of... (Review)
Review
Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vastly relies on laborious manual extraction from unstructured literature. In this paper, we propose COMMODAR, a machine learning-based literature mining framework for context-specific molecular relations using multimodal representations. The main idea of COMMODAR is the feature augmentation by the cooperation of multimodal representations for relation extraction. We leveraged biomedical domain knowledge as well as canonical linguistic information for more comprehensive representations of textual sources. The models based on multiple modalities outperformed those solely based on the linguistic modality. We applied COMMODAR to the 14 million PubMed abstracts and extracted 9214 context-specific molecular relations. All corpora, extracted data, evaluation results, and the implementation code are downloadable at https://github.com/jae-hyun-lee/commodar . CCS CONCEPTS: • Computing methodologies~Information extraction • Computing methodologies~Neural networks • Applied computing~Biological networks.
Topics: Data Mining; Machine Learning; PubMed; Publications
PubMed: 33106154
DOI: 10.1186/s12859-020-3396-y -
Annals of the New York Academy of... 2000In this note epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas...
In this note epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas of experience, such as folk biology and scientific biology, and hidden connections between central concepts of theoretical biology, such as function, semiosis, closure, and life.
Topics: Biological Evolution; Knowledge; Life; Models, Biological
PubMed: 10818570
DOI: 10.1111/j.1749-6632.2000.tb06278.x -
Philosophical Transactions of the Royal... Jul 2003What is abstraction? In our view, abstraction is generalization. Specifically, we propose that abstract concepts emerge as the natural product of associative learning...
What is abstraction? In our view, abstraction is generalization. Specifically, we propose that abstract concepts emerge as the natural product of associative learning and generalization by similarity. We support this proposal by presenting evidence for two ideas: first, that children's knowledge about how categories are organized and how words refer to them can be explained as learned generalizations over specific experiences of words referring to categories; and second, that the path of concepts from concrete to more abstract can be observed throughout development and that even in their more abstract form, concepts retain some of their original sensory basis. We illustrate these two facts by examining, in two kinds of learners--networks and young children--the development of three abstract ideas: (i) the idea of word; (ii) the idea of object; and (iii) the idea of substance.
Topics: Cognition; Concept Formation; Humans; Infant; Language Development; Learning; Pattern Recognition, Visual; Perception
PubMed: 12903655
DOI: 10.1098/rstb.2003.1306 -
Journal of Cognitive Neuroscience Sep 2011The role of sensory-motor systems in conceptual understanding has been controversial. It has been proposed that many abstract concepts are understood metaphorically...
The role of sensory-motor systems in conceptual understanding has been controversial. It has been proposed that many abstract concepts are understood metaphorically through concrete sensory-motor domains such as actions. Using fMRI, we compared neural responses with literal action (Lit; The daughter grasped the flowers), metaphoric action (Met; The public grasped the idea), and abstract (Abs; The public understood the idea) sentences of varying familiarity. Both Lit and Met sentences activated the left anterior inferior parietal lobule, an area involved in action planning, with Met sentences also activating a homologous area in the right hemisphere, relative to Abs sentences. Both Met and Abs sentences activated the left superior temporal regions associated with abstract language. Importantly, activation in primary motor and biological motion perception regions was inversely correlated with Lit and Met familiarity. These results support the view that the understanding of metaphoric action retains a link to sensory-motor systems involved in action performance. However, the involvement of sensory-motor systems in metaphor understanding changes through a gradual abstraction process whereby relatively detailed simulations are used for understanding unfamiliar metaphors, and these simulations become less detailed and involve only secondary motor regions as familiarity increases. Consistent with these data, we propose that anterior inferior parietal lobule serves as an interface between sensory-motor and conceptual systems and plays an important role in both domains. The similarity of abstract and metaphoric sentences in the activation of left superior temporal regions suggests that action metaphor understanding is not completely based on sensory-motor simulations but relies also on abstract lexical-semantic codes.
Topics: Adolescent; Adult; Brain Mapping; Cerebral Cortex; Concept Formation; Female; Humans; Image Processing, Computer-Assisted; Judgment; Magnetic Resonance Imaging; Male; Metaphor; Motor Activity; Neuropsychological Tests; Oxygen; Reaction Time; Reading; Recognition, Psychology; Statistics as Topic; Young Adult
PubMed: 21126156
DOI: 10.1162/jocn.2010.21596 -
Bioinspiration & Biomimetics Jul 2023In bio-inspired design, the concept of 'function' allows engineers and designers to move between biological models and human applications. Abstracting a problem to... (Review)
Review
In bio-inspired design, the concept of 'function' allows engineers and designers to move between biological models and human applications. Abstracting a problem to general functions allows designers to look to traits that perform analogous functions in biological organisms. However, the idea of function can mean different things across fields, presenting challenges for interdisciplinary research. Here we review core ideas in biology that relate to the concept of 'function,' including adaptation, tradeoffs, and fitness, as a companion to bio-inspired design approaches. We align these ideas with a top-down approach in biomimetics, where engineers or designers start with a problem of interest and look to biology for ideas. We review how one can explore a range of biological analogies for a given function by considering function across different parts of an organism's life, such as acquiring nutrients or avoiding disease. Engineers may also draw inspiration from biological traits or systems that exhibit a particular function, but did not necessarily evolve to do so. Such an evolutionary perspective is important to how biodesigners search biological space for ideas. A consideration of the evolution of trait function can also clarify potential trade-offs and biological models that may be more promising for an application. This core set of concepts from evolutionary and organismal biology can aid engineers and designers in their search for biological inspiration.
Topics: Humans; Biomimetics; Models, Biological; Engineering; Biology
PubMed: 37429293
DOI: 10.1088/1748-3190/ace5fb -
Canadian Family Physician Medecin de... Dec 1987The use of restraints is highly controversial. The authors first review the literature and emphasize the difference between the frequency of use of restraints in Canada...
The use of restraints is highly controversial. The authors first review the literature and emphasize the difference between the frequency of use of restraints in Canada and England. The very idea of restraints and their efficiency are being questioned. A brief description is given of the different types of restraints, and their advantages and disadvantages are mentioned. Special attention is given to alternative methods and a policy of least restraint is suggested.
PubMed: 20469473
DOI: No ID Found -
Topics in Cognitive Science Oct 2012From the late 1950s until 1975, cognition was understood mainly as disembodied symbol manipulation in cognitive psychology, linguistics, artificial intelligence, and the...
From the late 1950s until 1975, cognition was understood mainly as disembodied symbol manipulation in cognitive psychology, linguistics, artificial intelligence, and the nascent field of Cognitive Science. The idea of embodied cognition entered the field of Cognitive Linguistics at its beginning in 1975. Since then, cognitive linguists, working with neuroscientists, computer scientists, and experimental psychologists, have been developing a neural theory of thought and language (NTTL). Central to NTTL are the following ideas: (a) we think with our brains, that is, thought is physical and is carried out by functional neural circuitry; (b) what makes thought meaningful are the ways those neural circuits are connected to the body and characterize embodied experience; (c) so-called abstract ideas are embodied in this way as well, as is language. Experimental results in embodied cognition are seen not only as confirming NTTL but also explained via NTTL, mostly via the neural theory of conceptual metaphor. Left behind more than three decades ago is the old idea that cognition uses the abstract manipulation of disembodied symbols that are meaningless in themselves but that somehow constitute internal "representations of external reality" without serious mediation by the body and brain. This article uniquely explains the connections between embodied cognition results since that time and results from cognitive linguistics, experimental psychology, computational modeling, and neuroscience.
Topics: Brain; Cognition; Cognitive Science; Humans; Linguistics; Metaphor; Nerve Net; Thinking
PubMed: 22961950
DOI: 10.1111/j.1756-8765.2012.01222.x -
Studies in History and Philosophy of... Sep 2010The word 'environment' has a history. Before the mid-nineteenth century, the idea of a singular, abstract entity--the organism--interacting with another singular,...
The word 'environment' has a history. Before the mid-nineteenth century, the idea of a singular, abstract entity--the organism--interacting with another singular, abstract entity--the environment--was virtually unknown. In this paper I trace how the idea of a plurality of external conditions or circumstances was replaced by the idea of a singular environment. The central figure behind this shift, at least in Anglo-American intellectual life, was the philosopher Herbert Spencer. I examine Spencer's work from 1840 to 1855, demonstrating that he was exposed to a variety of discussions of the 'force of circumstances' in this period, and was decisively influenced by the ideas of Auguste Comte in the years preceding the publication of Principles of psychology (1855). It is this latter work that popularized the word 'environment' and the corresponding idea of organism--environment interaction--an idea with important metaphysical and methodological implications. Spencer introduced into the English-speaking world one of our most enduring dichotomies: organism and environment.
Topics: Biology; England; Environment; History, 19th Century; Life
PubMed: 20934645
DOI: 10.1016/j.shpsc.2010.07.003 -
SAGE Open Medicine 2018The idea that champions are crucial to effective healthcare-related implementation has gained broad acceptance; yet the champion construct has been hampered by... (Review)
Review
BACKGROUND/AIMS
The idea that champions are crucial to effective healthcare-related implementation has gained broad acceptance; yet the champion construct has been hampered by inconsistent use across the published literature. This integrative review sought to establish the current state of the literature on champions in healthcare settings and bring greater clarity to this important construct.
METHODS
This integrative review was limited to research articles in peer-reviewed, English-language journals published from 1980 to 2016. Searches were conducted on the online MEDLINE database via OVID and PubMed using the keyword "champion." Several additional terms often describe champions and were also included as keywords: implementation leader, opinion leader, facilitator, and change agent. Bibliographies of full-text articles that met inclusion criteria were reviewed for additional references not yet identified via the main strategy of conducting keyword searches in MEDLINE. A five-member team abstracted all full-text articles meeting inclusion criteria.
RESULTS
The final dataset for the integrative review consisted of 199 unique articles. Use of the term champion varied widely across the articles with respect to topic, specific job positions, or broader organizational roles. The most common method for operationalizing champion for purposes of analysis was the use of a dichotomous variable designating champion presence or absence. Four studies randomly allocated of the presence or absence of champions.
CONCLUSIONS
The number of published champion-related articles has markedly increased: more articles were published during the last two years of this review (i.e. 2015-2016) than during its first 30 years (i.e. 1980-2009).The number of champion-related articles has continued to increase sharply since the year 2000. Individual studies consistently found that champions were important positive influences on implementation effectiveness. Although few in number, the randomized trials of champions that have been conducted demonstrate the feasibility of using experimental design to study the effects of champions in healthcare.
PubMed: 29796266
DOI: 10.1177/2050312118773261 -
Perspectives on Psychological Science :... Nov 2016An important characteristic of knowledge is that it exists at multiple levels of abstraction. This article illustrates how different levels of abstraction influence...
An important characteristic of knowledge is that it exists at multiple levels of abstraction. This article illustrates how different levels of abstraction influence perception, comprehension, categorization, memory, and thought. Theories exist for how abstraction influences each of these cognitive processes, but there are few unifying principles for discussing these theories within a common conceptual framework. My proposed taxonomy examines three senses of abstraction: (a) an abstract entity is a concept that has no material referent, (b) abstraction focuses on only some attributes of multicomponent stimuli, and (c) an abstract idea applies to many particular instances of a category. The first refers to instances, the second to attributes of instances, and the third to classes of instances. Concrete mental representations consist of modal images for instances, equivalent attributes, and exemplars or episodes for categories. Abstract mental representations consist of amodal propositions for instances, distinctive attributes, and rules or prototypes or schema for categories. I first apply the taxonomy to words, pictures, and problems. The next section shows how categorization strategies combine with abstraction at the attribute, instance, and category levels. The subsequent section applies the taxonomy to hierarchical (subordinate, basic, superordinate) levels. A concluding section proposes directions for further development.
Topics: Classification; Comprehension; Concept Formation; Humans; Imagination; Language; Memory; Problem Solving; Space Perception
PubMed: 27899726
DOI: 10.1177/1745691616646304