{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,5]],"date-time":"2022-04-05T17:25:50Z","timestamp":1649179550321},"reference-count":8,"publisher":"World Scientific Pub Co Pte Lt","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2009,8]]},"abstract":"<jats:p> In this tutorial, we discuss two main algorithms for Hidden Markov Models or HMMs: the Viterbi algorithm and the expectation phase of the Baum\u2013Welch algorithm, and we describe ways to improve their na\u00efve implementations. For the Baum\u2013Welch algorithm we first present an implementation of the expectation computations using constant space. We then discuss the classical implementation of this calculation and describe ways to reduce its space usage to logarithmic and [Formula: see text], with their respective CPU costs. We also note where each respective algorithm can be parallelized. For the Viterbi algorithm, we describe [Formula: see text] and logarithmic space algorithms which increase CPU use by a factor of two and by a logarithmic factor respectively. We also present two recent heuristics for decreasing space use, which in practice lead to logarithmic space use. Classical version of Viterbi cannot be parallelized by splitting sequence in several subsequences, but we show a parallelization that works if we are willing to pay a significant extra CPU cost. Finally we show a very simple parallelization trick which enables full usage of multiple CPUs\/cores under the condition that they share memory. <\/jats:p>","DOI":"10.1142\/s0219720009004242","type":"journal-article","created":{"date-parts":[[2009,7,23]],"date-time":"2009-07-23T11:31:54Z","timestamp":1248348714000},"page":"737-754","source":"Crossref","is-referenced-by-count":2,"title":["A TUTORIAL OF TECHNIQUES FOR IMPROVING STANDARD HIDDEN MARKOV MODEL ALGORITHMS"],"prefix":"10.1142","volume":"07","author":[{"given":"DANIIL","family":"GOLOD","sequence":"first","affiliation":[{"name":"David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"DANIEL G.","family":"BROWN","sequence":"additional","affiliation":[{"name":"David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2012,1,25]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1109\/89.725318"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-6-231"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl659"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(70)90057-4"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492"},{"key":"rf7","author":"Newberg L. A.","journal-title":"Bioinformatics"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1145\/360825.360861"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/13.1.45"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720009004242","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T17:00:54Z","timestamp":1565197254000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720009004242"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,8]]},"references-count":8,"journal-issue":{"issue":"04","published-online":{"date-parts":[[2011,11,21]]},"published-print":{"date-parts":[[2009,8]]}},"alternative-id":["10.1142\/S0219720009004242"],"URL":"https:\/\/doi.org\/10.1142\/s0219720009004242","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,8]]}}}