Beefy Boxes and Bandwidth Generously Provided by pair Networks
XP is just a number
 
PerlMonks  

Re^6: Suffix-prefix matching done right (updated)

by LanX (Sage)
on Nov 06, 2021 at 16:06 UTC ( #11138511=note: print w/replies, xml ) Need Help??


in reply to Re^5: Suffix-prefix matching done right
in thread Suffix-prefix matching done right

> at least O(N^2)

A disagree, rather at most O(N*log N) for base64 input and a given max distance.

My algorithm based on Re: Suffix-prefix matching done right correctly calculated 1million overlaps with up to 6 errors in 2 seconds 53 sec , without being particularly tuned for speed.

You just have to avoid impossible matches right from the beginning and to bail out with the longest match.

Nobody needs all Levenshtein distances for all combinations.

Parameters:

my $n_tests = 1_000_000; my $error= 1+ int rand 5; my $A = rand64($n_err + 1 + rand 50); my $B = rand64($n_err + 1 + rand 50); my $prefix = rand64($n_err + 1 + rand 20); > Took: 2.20354223251343 sec

update
sorry

> Took: 53.5716695785522

I forgot a bail-out flag.

I'll try now strings with 2000 bytes ...

update
my $n_tests = 100_000; my $min_str = 2000;# 50; my $max_overlap = 500; #20; > Took: 56.4621770381927

as I said, it's still tuned for correctness not for performance

Cheers Rolf
(addicted to the Perl Programming Language :)
Wikisyntax for the Monastery

Replies are listed 'Best First'.
Re^7: Suffix-prefix matching done right (updated)
by NERDVANA (Pilgrim) on Nov 06, 2021 at 18:24 UTC
    OP said it could also be deletions and insertions. So the xor trick won't work. Without more information from OP, we can only guess, but I was guessing this was a genetics problem trying to build DNA sequences from fragments, and the mention of base64 was just mock data to test the algorithm. If the data can have random insertions, deletions, and swaps, then you need the full DP algorithm. *IF* the number of acceptable errors is low, then yes you can short-circuit it and maybe end up close to linear, but then there's stil the added complexity of deciding how much overlap gives the best result.
      > OP said it could also be deletions and insertions.

      Did he?

      Cheers Rolf
      (addicted to the Perl Programming Language :)
      Wikisyntax for the Monastery

        Hm. I guess that was also part of my assumption about it being a genetics problem.

Log In?
Username:
Password:

What's my password?
Create A New User
Domain Nodelet?
Node Status?
node history
Node Type: note [id://11138511]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others having an uproarious good time at the Monastery: (4)
As of 2022-01-24 14:52 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?
    In 2022, my preferred method to securely store passwords is:












    Results (64 votes). Check out past polls.

    Notices?