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From Words to Knowledge ORION Active Structure Two Approaches We could separate the process of turning words into knowledge into its components, or we could adopt a more holistic approach. ORION Active Structure A Sequence of Activities Words POS Tags Grammar Semantics Knowledge This approach segments the process into separate parts, each of which is blind to all the others. This seems easier conceptually, but is obviously not what people do in reading text. ORION Active Structure The Holistic Approach Global Knowledge Semantics Words Active Structure Grammar Local Knowledge The lexing, grammar, semantic and structure-building processes proceed simultaneously and synergistically, opportunistically using any information coming from any direction ORION Active Structure The Basic Elements These are the basic elements of Active Structure - variables, operators, links, values flowing in the structure ORION Active Structure A Common Substrate PARSE The basic elements of Active Structure can also be seen as Entities, Relations and States These three elements are adequate to model everything - including the grammar of language and the world of objects ORION Active Structure The Reading Process A document is read, paragraph by paragraph, sentence by sentence, word by word. As the words are read, they are turned into objects that can be manipulated - objects that have the properties both of words and of the objects they represent - a ligand, a gene The word objects are assembled through grammar into larger objects - receptor or gene structure And into larger structures, using the relations between the objects provided by nouns and verbs ORION Active Structure Transformation changes in the conformation of the Tsr dimer induced by serine binding improve methylation efficiency ORION Active Structure Building Structure Four Word Noun Phrase Start The Red Car When a single possible structure match is found, an invocation of the structure is built, leaving a new BRIDGE operator to look for higher level matches ORION Active Structure Stop Next Symbol Prep Phrase Noun Phrase Start The Hat Verb Phrase Pre position Was On Noun Phrase Pre position Head Of Noun Phrase Man The Next Symbol depends on the local structure - run down from the current symbol, then run up again if other structure exists, otherwise jump across a PARSE ORION Active Structure Stop Harpooning the Model When the noun phrase is recognised, the objects it joins are searched for connection - one is found for animal and colour through ATTRIBUTE, so the same relation joining the objects is searched for in the model, and a unique match is “harpooned” for use with relations the type of object changes the grammar ORION Active Structure Automatic Phasing Four Word Noun Phrase Start The Red Car A BRIDGE operator doing a long match may find not all the information is available If so, it puts a connection on the missing information and waits to be re-activated ORION Active Structure Stop In the Process of Building Part of a sentence under construction - hundreds of different active structures are cooperating in the process building up, cutting out, reversing connections ORION Active Structure Tight Integration The structure combines lexical information, grammar and semantics - we pick up the fact that a word is a noun because it is an Entity, we know something isn’t a Material because the Verb says not. This tight and immediate interweaving of lexical, grammatical and semantic analysis allows us to do things that are not possible with a static sequential approach. ORION Active Structure Scientific Sentences Are Complex The synergistic effect of serine and CheW binding to Tsr is attributed to distinct influences on receptor structure; changes in the conformation of the Tsr dimer induced by serine binding improve methylation efficiency, and CheW binding changes the arrangement among Tsr dimers, which increases access to methylation sites. ORION Active Structure Grammar Is Not Enough Grammar alone would turn meaningful scientific text into sludge - a participial phrase “induced by...” has to be anchored on the right object, a relative pronoun “which” has to be anchored on the relation The reading process demands that domain knowledge be available at every turn - knowledge that is held in object hierarchies and relations, and which is seamlessly intermingled with grammatical knowledge during the parsing ORION Active Structure What Does It Rely On The paradigm relies on dynamic construction and destruction of active structure, where operators in the structure respond to their local environment by changing the local topology, and then respond to the changed environment, and so on. Each operator can only transmit information through its links, change its connections, add structure or destroy itself. Their interaction suffices to cause all the necessary processes to proceed in parallel, in an opportunistic and synergistic manner. ORION Active Structure Typical Domain Knowledge Model The model is built out of the same variables, operators, links as the grammatical and semantic structures, so it can interact with them Greece Info (GIS) Find distance between site and epicentre, local conditions, etc. Attenuation Acceleration attenuation based on magnitude, distance and local site conditions Intensity/ Damage Relations between acceleration, intensity and damage ratio Earthquake Event ORION Active Structure Relations between magnitude and frequency, building type, number of floors and natural frequency Frequency/ Amplification Genetic Knowledge Anatomy ABCA1: ATP-binding cassette, sub-family A (ABC1), member 1 Genes LocusID: 19 Overview Family ABC (transporter across membranes) Subfamily ABC1 (members ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White) Gene ABCA1 Protein NP_005493 Substrate Cholesterol Function cholesterol efflux pump associated lipid removal pathway Mutation causes Tangier’s disease, familial high-density lipoprotein deficiency. Liver Brain ? The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump in the cellular lipid removal pathway. Mutations in this gene have been associated with Tangier's disease and familial high-density lipoprotein deficiency. Diseases Kidney Eye Brain Cortex ABC HKT PFIC Proteins PKC NP_0001 NP_0047 Chromosome: 9 mv Cytogenetic: 9q31.1 RefSeq The structure is used to understand the text then the text is used to extend the structure ORION Active Structure Liver FF Why Do This The automated process of Information Extraction needs to be in the same state as a knowledgeable human reader at every point in the text, so inferences about alternatives and anaphora are made on the same basis - the basis on which the writer expects them to be made. The automated process also needs the ability to backtrack when reading more text refutes assumptions already built into any part of the structure. ORION Active Structure Is It Really So Different We are asserting that knowledge can only be captured in active structure - structure that is capable of adapting itself to its environment. Efforts at capturing knowledge in static structure founder on two reefs - the pieces of structure will not fit together statically, and an algorithm that could manage their combination would be more complex than the combination of the pieces, and is thus unmanageable. Active Structure avoids both problems - the pieces adapt to each other, and the behavior of the combination is managed by the interaction of the pieces. ORION Active Structure ORION Active Structure