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PubMed · 14901765

Mechanical minds.

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G JEFFERSON. 1952. Mechanical minds.. https://pubmed.ncbi.nlm.nih.gov/14901765/

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PASBio: predicate-argument structures for event extraction in molecular biology.

BACKGROUND: The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction. RESULTS: We introduce PASBio by extending a model based on PropBank to the MB domain. The hypothesis we explore is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions. We chose predicates describing gene expression, molecular interactions and signal transduction events with the aim of covering a number of research areas in MB. Analysis was performed on sentences containing a set of verbal predicates from MEDLINE and full text journals. Results confirm the necessity to analyze PAS specifically for MB domain. CONCLUSIONS: At present PASBio contains the analyzed PAS of over 30 verbs, publicly available on the Internet for use in advanced applications. In the future we aim to expand the knowledge base to cover more verbs and the nominal form of each predicate.

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Love-hate for man-machine metaphors in Soviet physiology: from Pavlov to "physiological cybernetics".

This article reinterprets the debate between orthodox followers of the Pavlovian reflex theory and Soviet "cybernetic physiologists" in the 1950s and 60s as a clash of opposing man-machine metaphors. While both sides accused each other of "mechanistic," reductionist methodology, they did not see anything "mechanistic" about their own central metaphors: the telephone switchboard metaphor for nervous activity (the Pavlovians), and the analogies between the human brain and a computer (the cyberneticians). I argue that the scientific utility of machine analogies was closely intertwined with their philosophical and political meanings and that new interpretations of these metaphors emerged as a result of political conflicts and a realignment of forces within the scientific community and in society at large. I suggest that the constant travel of man-machine analogies, back and forth between physiology and technology has blurred the traditional categories of the "mechanistic" and the "organic" in Soviet neurophysiology, as perhaps in the history of physiology in general.

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