Concept

Alphabet size — where it appears

How many distinct symbols a text is drawn from, which decides how far a mismatch lets a pattern jump and how long two random strings agree. It appears in almost every bound in this field and is almost never stated with one, which makes a quoted matching cost hard to compare across texts.

Named by 18 essays across 9 fields — each of them below, with the objects they name alongside it.

characters examinedNaive scan520,25663.51 per text characterKnuth–Morris–Pratt16,3211.99 per text characterBoyer–Moore–Horspool8,1290.99 per text characterRabin–Karp00.00 per text characterone unit = one character comparisonone matcher read no characters at all

The shift the pattern already knows

On a text of 8,192 characters the naive scan examines 520,256 of them and Knuth–Morris–Pratt examines 16,321 — a factor of 32, and 16,321 is 99.6% of the 2n that no input can push it past. On ordinary random text the same two algorithms examine 20,862 and 20,833. Both measurements are of the same pair of algorithms and only one of them is the reason anybody uses the second.

text · Symbol
one read per text character24816326495alphabet size, m = 8characters read ÷ text length0.01.12.2Naive scanKnuth–Morris–PrattBoyer–Moore–Horspoolone unit = one character comparison · n = 20,000, m = 8Horspool's best here: 0.132 per character

The text that answers without reading it

Boyer–Moore–Horspool finds every occurrence of an eight-character pattern in a twenty-thousand-character text while examining 2,985 characters. Not 2,985 comparisons of eight characters each — 2,985 characters, 0.149 per character of text. It is a correct algorithm returning a complete answer about a text it has mostly not looked at, and the reason it can is a property of the alphabet rather than of the algorithm.

text · Symbol
gactacgatgattacagt112223334244352461647one unit = one subproblem given a value21 matching pairs, 21% of the rectangle

The cells that were never worth having

Two three-hundred-character strings over twenty-six letters give a table of 90,601 cells, and 3,421 of them are pairs of positions whose characters agree. Only those can lengthen anything. A method that enumerates exactly those computes a twenty-sixth of the table — and on a two-letter alphabet it computes half of it and is worse than the table it replaced.

tables · Table
10010³10⁴10⁵errors allowed, kacts01234index walkthe whole table4,000 characters · m = 16 · 4 symbolscrossing at k = 4

The branches an error opens

The tree multiplies by 19.6 for the first error, 12.3 for the second, 10.3 for the third and 8.8 for the fourth. A branching factor of four on a sixteen-character pattern would predict sixty-four, and the gap between sixty-four and eight is the intervals emptying.

bounds · Distance
k = 0k = 1k = 2k = 3k = 4k = 5k = 6q = 223211917151311q = 3221916131074q = 4211713951-3q = 520151050-5-10q = 6191371-5-11-17q = 81791-7-15-23-31a shaded cell is a threshold of zero or less: every window proposedt = m + 1 − q(k+1) · m = 2411 collapsed cells

The q-grams an error cannot destroy

A pattern of twenty-four characters holds twenty-one four-grams. Two errors can destroy at most eight of them, so any occurrence with two errors still shares thirteen — and a filter that keeps only the windows sharing thirteen proposes 104 of 3,977 and computes 16,744 table cells instead of 96,000.

text · Distance
010010³10⁴interval extensions48.1%68.5%69.8%errors allowed · share removed belowno pruningpruned on D4,000 characters · m = 1669.8% removed at k = 3

The branch that cannot reach an answer

Seventy-two rank operations over the pattern remove 27,906 of the 39,957 interval extensions a bounded-error index walk performs — 70% of the tree, at a budget of three. The share grows with the budget, which is what a pruning has to do to be worth its cost.

bounds · Distance
0100200300102030distinct symbols in the intervalbit-vector ranksthe loop: 320the descentsigma = 32 throughout32x down to 5.16x

Proportional to the answer, not the alphabet

At a fixed alphabet of thirty-two, a loop costs three hundred and twenty ranks whether one symbol is present or all of them. The descent costs ten and sixty-two. The experiment has to move the answer without moving the alphabet, and the obvious sweep moves both.

floors · Symbol
run together38,400 bitsσ 21 · 5 bitsone separator38,470 bitsσ 22 · 5 bitsa separator each46,164 bitsσ 35 · 6 bits15 documents of 512 charactersthe separators are the only differenceEnglish-like · 15 documents1.20x for the distinct marks

One separator, or one for each

A shared separator costs one alphabet symbol and is free. Fifteen distinct ones take the alphabet from twenty-two to thirty-five, which crosses a power of two, so every character of every document costs a sixth bit — 1.2 times the packed collection, to tell the boundaries apart.

space · Document
one text16 short documentsprosecopies of one baseprose, one textr/n 0.2996z/n 0.1273prose, many short documentsr/n 0.3053z/n 0.1301copies of one base, run togetherr/n 0.0638z/n 0.0354one copy per documentr/n 0.0768z/n 0.04188,192 characters throughoutthe outlined cell is the one that was empty

The cell nobody filled

Every structure here was measured either on one long repetitive text or on prose cut into short documents. The collection that is both is a two-by-two with one empty corner, and what is in it is not the product of its margins.

text · Document
10⁴0.1charactersphrases of the parse, per charactershuffled: 1.45xthe collection: 4.71x4,111 to 65,551 charactersworth 3.24x after the control

What repetition is worth once the logarithm is gone

On prose, nearly three quarters of the fall in phrases per character with size is arithmetic that any text pays. On a collection built of copies it is a fifth, and what is left is a factor of three that is genuinely the arrangement.

text · Document
short by 133.6% of pairsshort by 211.2% of pairsshort by 411.2% of pairsthe same shift7994.0% of pairspatterns of 10 over four symbolsthe published rule is never the larger of the twoshift decisions84 pairs · 21 nodes

What the approximation gives up

Compared at every one of the 3,736 decisions a search could ask about, the published shift rules and the exact ones agree at all of them on a set of 128 patterns. At two patterns they differ at five of 84, by up to four positions — and the run reads 6.3% more characters.

wrong · Symbol
binary · sigma 22.00x2 against 4dna · sigma 42.67x6 against 16protein · sigma 204.76x42 against 200latin · sigma 264.81x54 against 26064-position interval2.00x to 4.81x

Two at binary, five at twenty-six

The saving is a factor in the alphabet, so a two-symbol alphabet gets two. Approximate matching in this field is mostly done on DNA, which sits near the bottom of the list at 2.7.

bounds · Symbol
025507510000.50011.502errors permittedfactor against the published loop64.5%55.8%74.7%the walk: 11xthe descentthe label is the shareof dead extensions6 patterns · sigma 2198x to 105x

Flat in the budget, and not

One saving is eleven times at every error budget, because it is a property of the alphabet. The other moves between ninety-eight and a hundred and five, because it follows the share of extensions that find nothing. Two savings, two shapes, and neither line crosses the other.

bounds · Distance
1101000.1documentsruns of the transform, per characterprose: 1.10xcopies: 1.02x8,192 characters, cutthe control rises further

A boundary that costs nothing

A separator occurs nowhere else in the collection, so it must break a phrase that would have spanned it. Cutting a repetitive text into a hundred and twenty-eight documents raises its run count by two per cent, and cutting prose raises it by ten.

wrong · Document
051015255075100125documentsdistinct characters the documents end with+7+52+162+293+4+-1+9+19prosecopies of one basethe label is the runsthe cut added128 documents0.15 against 2.31 runs a separator

The price of a boundary is what precedes it

A separator sorts before everything, so its rows sit at the top of the suffix array and hold the documents' last characters. What a document boundary costs the transform is the entropy of the character in front of it, and nothing else.

structures · Document
run together1.00xsigma 21 · 5 bitsone separator1.00xsigma 22 · 5 bitsa separator each1.20xsigma 36 · 6 bitsruns 1.00xruns 1.00xruns 1.02x16 documents of 512 characterspacked bits, against running them together

Two currencies for one separator

Giving every document its own boundary marker costs a fifth of the packed text and three per cent of the run count. Both numbers are right, they are about the same change, and which one a collection pays depends on a structure nobody named.

space · Document
acdefghijklmnopqrstuvwyzroot24 of 26 symbols present54 ranks · 51 nodes

Asking about symbols that are not there

A search extends an interval by every character of the alphabet, and on a deep branch almost all of them produce an empty interval. That is a full rank walk whose entire result is the discovery that nothing was there.

indexes · Symbol
02040608000.50011.502errors permittedbranches that find nothing, per cent5.75x6.98x9.22xthe label is thesaving at that budget8 patterns · 8 characters31.3% to 74.9%

A looser budget wastes a larger share

More errors permitted means more work, and the fraction of that work which was never going to help rises with it — from thirty-one per cent at no errors to seventy-five at two. The saving is worth most where the search is most expensive.

practice · Symbol

Named alongside it

The objects these essays reach for when they reach for this one.

Backtracking searchBurrows-wheeler runsInterval symbolsMeasurementMeasurement designRepetitionSelf-indexSeparatorApproximate matchingDescentDocument collectionError budget

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