Finding biologically relevant information using ADIOS发现生物学相关信息用再见.pptVIP

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Finding biologically relevant information using ADIOS发现生物学相关信息用再见.ppt

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Finding biologically relevant information using ADIOS发现生物学相关信息用再见

Finding biologically relevant information using ADIOS ThaiBinh’s final project for CBB545: The current state of affairs in natural language processing NLP: Converting human language into representations that are easier for computers to understand Most natural language processing requires a tagged training set Tagging = time consuming/costly ADIOS “Unsupervised learning of natural languages” ADIOS: Automatic distillation of structure Input: A corpus of characters (most likely, untagged sentences) Output: A grammar A very quick primer on grammars A set of “rules” for making a “sentence” Ex. A very quick primer on grammars We can visualize the expansion as a tree, and read the leaves A very quick primer on grammars We can visualize the expansion as a tree, and read the leaves ADIOS The system builds a graph using the first sentence With each successive sentence, it tries to find overlapping “subpaths” (patterns) ADIOS Also try to generalize the path by looking for equivalence classes Search for patterns and equivalence classes until no new ones are found ADIOS: A quick example Input a corpus of sentences ADIOS: A quick example Output is a grammar Two different grammars: Same end result ADIOS Able to generate sentences using the grammar it created Can test if new sentence fits one of the grammar rules Can be applied to wide variety of domains Bible in various languages Classify protein function based on amino acid sequence The Project Use ADIOS to create grammar rules from biomedical sentences Look for gene-gene associations Look for gene-disease associations Infer information about a pair of genes in an unseen sentence based on its sentence structure (pattern) AbnerFind mentions of genes MetamapFind mentions of diseases The Project: Input Replace any mention of a gene with a generic term Ex. The Project: Input Replace any mention of a gene/disease with a generic term Ex. “Tagging” the patterns “Tagging” the patterns “Tagging” the patterns Seeing a new sen