machineboss

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HMMER weights IUPAC degenerate emissions using the reciprocal of the perplexity of the underlying match state (see `esl_abc_FExpectScore` function in HMMER3 source) This has the effect that the "score" for...

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Graph-grammar decoding

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Find an "ideal" generator by beginning with a beam search, then iteratively & greedily applying the best expansion of a given graph grammar on the current generator, keeping the generator...

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See https://www.biorxiv.org/content/early/2018/08/16/392639

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The current intersection algorithm requires that both transducers be recognizers (i.e. empty output alphabets). But this is not necessary, because - the current algorithm should work even if only one...

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https://cancer.sanger.ac.uk/cosmic/fusion https://cancer.sanger.ac.uk/cosmic/help/fusion/overview https://cancer.sanger.ac.uk/cosmic/help/file_download

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Simulator

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All cases (conditioned on input, output, both, or neither) can be reduced to the null machine (empty input & output) by appropriate compositions with generators/acceptors. Then, that null machine can...

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Currently it's not idempotent

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