From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: X-Original-To: caml-list@yquem.inria.fr Delivered-To: caml-list@yquem.inria.fr Received: from nez-perce.inria.fr (nez-perce.inria.fr [192.93.2.78]) by yquem.inria.fr (Postfix) with ESMTP id BD1C6BB83 for ; Tue, 4 Jul 2006 18:55:23 +0200 (CEST) Received: from nf-out-0910.google.com (nf-out-0910.google.com [64.233.182.190]) by nez-perce.inria.fr (8.13.6/8.13.6) with ESMTP id k64GtOJe012280 for ; Tue, 4 Jul 2006 18:55:24 +0200 Received: by nf-out-0910.google.com with SMTP id k27so987431nfc for ; Tue, 04 Jul 2006 09:55:23 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=googlemail.com; h=received:message-id:date:from:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=F2ubiCFnWqZMdYfKjP1vC4bJ0V5wGENObn6CbJxAWC42r5cmIAkbmxjqUujC/MU4MrwniTcevgWgX7yVPLpd8arU6R+1quYaggH7YBBzJALlu5Vyr0kw2x2yW/nEWvjYEQmYFtqyjaC7IaNzFMJu2ia61MHH1aOduI9LCEygmdc= Received: by 10.48.218.19 with SMTP id q19mr3464681nfg; Tue, 04 Jul 2006 09:55:23 -0700 (PDT) Received: by 10.48.220.18 with HTTP; Tue, 4 Jul 2006 09:55:22 -0700 (PDT) Message-ID: Date: Tue, 4 Jul 2006 18:55:22 +0200 From: "Andreas Biegert" To: caml-list@yquem.inria.fr Subject: Re: [Caml-list] Package with multidimensional AND sparse matrices? In-Reply-To: <200607041103.59059.jon@ffconsultancy.com> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline References: <200607041103.59059.jon@ffconsultancy.com> X-j-chkmail-Score: MSGID : 44AA9D7C.001 on nez-perce : j-chkmail score : X : 0/20 1 X-Miltered: at nez-perce with ID 44AA9D7C.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Spam: no; 0.00; matrices:01 computes:01 computes:01 alignment:01 sequences:01 computed:01 non-zero:01 non-zero:01 sequences:01 hashtables:01 matrices:01 hashtable:01 ocaml:01 beginner's:01 ocaml:01 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on yquem.inria.fr X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=disabled version=3.0.3 Since the algorithm computes alignemnts in most casses the pattern of access will be adjacent tuples, for example (i,j,k,l) (i,j,k-1,l-1) etc. But it does not have to be that way. The only contstraint that holds for sure is i: > On Tuesday 04 July 2006 08:46, Andreas Biegert wrote: > > Well, in short: the algorithm computes the optimal multiple alignment > > of up to n protein sequences with maximum length L. The > > straightforward and theoretically optimal approach to solve this > > problem is by dynamic programming, therefore the time and space > > complexity is O(L^n). I managed to come up with a pretty good > > heuristic that lets me boil down the number of cells that need to be > > computed giving me a complexitiy of O(L^2) instead of O(L^n), in fact > > I can even manually adjust the number of nonzero entries in the > > matrix. In the 2000*2000*2000*2000 matrix only at most 2000 cells will > > be non-zero. Furthermore for all non-zero cells M(i,j,k,l) holds > > i > program has to run under 5min. An estimation of the time requirements > > given the number of sequences n and masimum lengths L is: > > > > 24 * L^2 * T_x * 2^(n+1) - 1 > > with T_x being about 100ns > > Ok. What patterns of access will there be? > > > For n=4 and L=2000 I get just about 5min. Would it be a bad idea to > > use Hashtables all the way instead of matrices? > > No, I don't think so. If you need more performance then you can always change > things later. I'd concentrate on getting a working algorithm first. > > > Accessing elements in > > a hashtable has O(1), right? > > Roughly, yes. :-) > > -- > Dr Jon D Harrop, Flying Frog Consultancy Ltd. > Objective CAML for Scientists > http://www.ffconsultancy.com/products/ocaml_for_scientists > > _______________________________________________ > Caml-list mailing list. Subscription management: > http://yquem.inria.fr/cgi-bin/mailman/listinfo/caml-list > Archives: http://caml.inria.fr > Beginner's list: http://groups.yahoo.com/group/ocaml_beginners > Bug reports: http://caml.inria.fr/bin/caml-bugs >