index4j

This repository is a Java library developed by Dynatrace that implements the FM-Index succinct data structure. The FM-Index takes advantage of the relationship between the suffix array and the Burrows-Wheeler transform to enable both compression and fast queries.

This index is specifically suited for compressing and querying text files without requiring prior tokenization. This means that you can compress a text file and then query it for arbitrary substrings without the need to fully decompress it, i.e., only the compressed size is required to be in memory. Furthermore, query performance depends on the number of located matches and total decompressed bytes, rather than whether the query is aligned with a particular token.

In addition, this repository also contains further data structures for working with bit vectors and integer sequences in Java.

Content

First steps
Supported data structures
How-to and example use cases
Benchmarks
Details about the data structures
About this project

First steps

TODO add dependency on maven

Supported data structures

Fm-Index: supports count, locate, extract and extractUntilBoundary (along with its left and right variations) with arbitrary patterns while compressing your data. In the case of logs, roughly 20% of the input size is required to store both data and index.
RrrVector (Raman, Raman & Rao): compressed bit vectors which both compress and enables rank and select queries.
SuffixArray: supports querying arbitrary patterns on input text requiring O(n logn) time and O(5n) space.
Wavelet FBB: Fast wavelet trees that compress and support rank and select queries on arbitrary sequences.
Burrows-Wheeler transform: enables calculating the BWT of inputs as well as compute redundancy metrics.

How-to

Using the FM-Index

The following examples show how to make use of the provided FM-Index implementation. Note that both compression and query speed are controlled by the sample rate parameter (find more details here). In essence, a larger sample rate results in better compression but slower query performance, and viceversa. Note that "larger" here means "larger distance" between samples, and therefore, actually translates into fewer samples.

Creating an FM-Index

The following snippet creates an FM-Index for a char array text using a sample rate of 32 and enabling the extraction/decompression of the index.

char[] text = ...
FmIndex fmi = new FmIndexBuilder()
        .setSampleRate(32)
        .setEnableExtraction(true)
        .build(text);

To get some statistics, we can do the following:

System.out.println(fmi.getAlphabetLength());                            // how many symbols
System.out.println(fmi.getInputLength());                               // the length of the input `text`
int size = Serialization.writeToByteArray(FmIndex::write, fmi).length;  // actual compressed size
System.out.println((size * 100 / fmi.getInputLength()) + "%)");         // relative size to the input

Note that the original input string is no longer required to perform any query at all, and in fact the whole input can be retrieved back by decompressing or extracting between 0 and |text|.

Counting occurrences of a pattern

Count how many times the pattern DEBUG (with spaces before and after) is in the input data.

char[] pattern = " DEBUG ".toCharArray();
System.out.println(fmi.count(pattern));

Locating the positions of an occurrence

Using the previous pattern, find at most 10 matches and their position in the original input.

int[] locations = new int[10];
int found = fmi.locate(pattern, 0, pattern.length, locations, 10); // find max. 10 matches
System.out.println(found); // print number of matches
System.out.println(Arrays.toString(locations)); // print the locations of the matches

Extracting key-value pairs

Using the previously found matches and locations, extract the right-most string containing the match and until a comma ',' is found.

char[] destination = new char[100]; // maximum length per extraction
for (int i = 0; i < found; i++) {
    int length = fmi.extractUntilBoundaryRight(locations[i] - 1, destination, 0, ','); // extract previous locations until finding a comma
    System.out.println(new String(destination, 0, length)); // print the extracted string
}

Extracting whole records

Extracting the full string, left and right from every match until a line separator '\n' is found.

char[] destination = new char[512]; // maximum length per extraction 
for (int i = 0; i < found; i++) {
    int length = fmi.extractUntilBoundary(locations[i], destination, 0, '\n');
    System.out.println(new String(destination, 0, length));
}

Serializing

All data structures (except the naive WaveletTree) can be serialized and deserialized via the SerializationReader and the SerializationWriter, respectively.

You can do so as shown below:

FmIndex fmi = new FmIndexBuilder().build(...);
byte[] serialized    = Serialization.writeToByteArray(FmIndex::write, fmi);
FmIndex deserialized = Serialization.readFromByteArray(FmIndex::read, serialized);

Using RRR Bit vectors

Similarly to the FM-Index, RRR bit vectors also make use of the sample rate. A higher sample rate results in using less space but at the expense of slower rank and access queries. In particular, a sample rate of e.g. 32 will result in saving a prefix sum every 32 bits, as well as saving the position of offsets every 32 bits. Therefore, in the worst case, up to 32/BLOCK_SIZE blocks need to be traversed before finding the rank or access answer.

Creating RRR Bit vectors

We have two options to create RRR bit vectors: either through an array of integers, which we interpret as a sequence of bits (e.g. if the int value is 2 then we have a bit sequence of 010...000000) or creating it through an already existing BitVector from the sux4j library. For example, using a sequence of integers and a sample rate of 32:

int[] array = new Random().ints(1000).toArray();
RrrVector rrr = new RrrVector(array, 32);

Or from a BitVector:

int lengthInBits = 1000;
BitVector bv = LongArrayBitVector.getInstance().length(lengthInBits);
// Fill in some values
Random random = new Random();
for (int i = 0; i < lengthInBits; i++) {
    bv.set(i, random.nextBoolean());
}
// Create it
RrrVector rrr = new RrrVector(bv, 32);

Ranking zeros or ones

The following snippet shows how to count the number of 1's or 0's until a given position (exclusive).

int[] array = ...
RrrVector rrr = new RrrVector(array, 32);
System.out.println(rrr.rankOnes(10)); // Number of 1's until position 10
System.out.println(rrr.rankZeroes(50)); // Number of 0's until position 50

Access an arbitrary position

Get the value of the bit at position i:

int[] array = ...
RrrVector rrr = new RrrVector(array, 32);
System.out.println(rrr.access(7)); // Get the bit value as a boolean (true or false) of the bit sequence at position 7

Serializing

Similar to the FM-Index, we can serialize and deserialize our RRR bit vectors as follows:

int[] array = ...
RrrVector rrr = new RrrVector(array, 32);
byte[] serialized      = Serialization.writeToByteArray(RrrVector::write, rrr);
RrrVector deserialized = Serialization.readFromByteArray(RrrVector::read, serialized);

Using Wavelet trees

Currently, two implementations of the wavelet tree are supported. However, only the Fixed-block boosting wavelet tree should be used since its performance and memory consumption is much better than the vanilla wavelet tree implementation.

The Fixed-block boosting wavelet tree (FBB-WT in advance) also uses the sample rate parameter since it is composed of multiple RRR bit vectors.

Creating FBB-WT

The FBB-WT can be built from either a sequence of chars or shorts. In any case, both are interpreted as symbols and should be mapped to a sequence {0,1,2, ..., n} such that v_{i+1} = v_{i} + 1 for all i. This allows for a larger alphabet, up to 32,768 different symbols, whereas otherwise if there is a single symbol with a value above 32,768 it will fail. The following snippet shows how to create an FBB-WT without such mapping:

char[] text = "This is an example".toCharArray();
WaveletFixedBlockBoosting wavelet = new WaveletFixedBlockBoosting(text);

And the following includes a mapping:

char[] text = "Los erizos pasean junto a la torre".toCharArray();

Map<Character, Short> map = new HashMap<>();
short code = 0;
for (char c : text)
    if (map.putIfAbsent(c, code) == null) ++code;

short[] mappedSequence = new short[text.length];
for (int i = 0; i < text.length; i++)
    mappedSequence[i] = map.get(text[i]);

WaveletFixedBlockBoosting wavelet = new WaveletFixedBlockBoosting(mappedSequence);

Ranking symbols

By generalizing the bit vector structure, the FBB-WT is able to rank any symbol:

char[] text = ...
WaveletFixedBlockBoosting wavelet = new WaveletFixedBlockBoosting(text);
long howManyZs = wavelet.rank(60, map.get('z')); // counts how many times the letter 'z' appears before position 60

Accessing symbols

We can also retrieve the original symbol at position i:

char[] text = ...
int i = 33;
WaveletFixedBlockBoosting wavelet = new WaveletFixedBlockBoosting(text);
long ithAndSymbol = wavelet.inverseSelect(i); 
// Note that this long contains two ints: the first one is the number of the occurrence and the second one is the symbol value
assert text[i] == (char) ithAndSymbol; // by casting it to char we are taking the symbol bytes only

Serializing

Same approach as in previous occasions:

char[] text = ...
WaveletFixedBlockBoosting wavelet = new WaveletFixedBlockBoosting(text);

byte[] serialized = Serialization.writeToByteArray(WaveletFixedBlockBoosting::write, wavelet);
WaveletFixedBlockBoosting deserialized = Serialization.readFromByteArray(WaveletFixedBlockBoosting::read, serialized);

Benchmarks

The jmh package contains ready-to-run benchmarks for the FM-Index, the RRR bit vector and the Suffix Array. Most of the classes contain results which were run with the Android.log dataset of the public repository loghub. The benchmarks are divided into three types:

Ingest: Measures how long it takes to create the data structure given the input.
Throughput: Measures the query performance of the data structure as function of the sample rate.
SerializedSize: Measures the size of the data structure once it is serialized.

The additional state type simply holds the state necessary to run the benchmarks. The benchmarks jar can be built with the following command:

./gradlew clean jmhJar

And then run as follows:

java -jar indices/build/libs/benchmarks.jar <regex matching name of benchmark> -p parameter1=value1 -p parameter2=value2 ...

For example:

java -jar indices/build/libs/benchmarks.jar FmIndexSerializedSizeBenchmark -p data=Android.log -p sampleRate=8,16,32,64

Infrastructure

The following benchmarks were run with 3 forks, each one running 5 warmup iterations and 10 measurement iterations. They were run on a Xeon W-10885@2.40GHz with disabled Turbo Boost and 64 GB of RAM. Note that a more automated approach for benchmarking is intended for future work.

Trade off plots between speed and space

The following plots summarize the general behavior of the FM-Index data structure for the locate and extract queries. The Android.log dataset of the public repository loghub was used. It contains exactly 1,555,005 lines, totalling 184 MB of data with an alphabet containing over 1,000 different symbols (letters).

Locate queries

The plot depicts the number of microseconds required for locating a variable number of matches (either 1, 10, 100 or 1,000) as a function of the size, which depends on the value of the sample rate. The red dotted line in the zoomed-in region shows the performance that can be achieved if using a sample rate that results in roughly 25% of the original input size (including both index and data).

As can be seen, locate queries can be done in microseconds time depending on sample rate and output size, for example, at 25% of the original size (achieved approximately with a sample rate of 64) gets us to 100 microseconds per output match. The higher the number of output matches, the better the per-match average location time, e.g., for 100 matches it goes down to ~25 microseconds per match.

Extract/decompress queries

Similarly to locate queries, the extract/decompress queries are also affected by sample rate. At a 25% size (or sample rate of 64), we can extract at a rate of one symbol per ~2 microseconds. This translates into the fact that if we need to extract a full log record of ~300 characters, we can expect roughly ~300 to ~600 microseconds, or half a millisecond. On the contrary, if working with key/value pairs of e.g. size 30 characters, then ~30 to ~60 microseconds per extraction is reasonable.

Compression evaluation

How much can we compress the FM-Index while still being queryable depending on the sample rate? First, when the size becomes asymptotic it is worth noting that the queries become much slower. However, this can be still be useful if for example the use case requires higher compression and only sporadic querying. For reference, the close to theoretical compression limit with Z-standard is included, at two levels of compression. Notice that the FM-Index is the index as well (not just data, as opposed to the Z-standard compression). It can be seen that the FM-Index requires around ~4 times the size of the Z-standard compressed file (which already represents only 25% of the original file size) when used with reasonable sample sizes (such as 64 or 128), which still offer high speed queries. Nevertheless, when reaching the compression limits at a sample rate of ~1024 or higher, the FM-Index only requires ~2 times the space.

Index construction runtime

The construction time of the FM-Index depends on building multiple other data structures which, although all linear in runtime, still contribute towards a larger constant build time. In this line, you can expect the provided implementation of the FM-Index to process inputs at roughly 2 MB/s (see the benchmark for more details). This translates into a 200 MB input text requiring approximately a minute and a half to build the index. The construction time is also affected by the sample rate but to a much smaller degree in comparison with the compression or query performance, and can be almost ignored for practical purposes. Luckily, building the index is required only once per input.

Details

FM-Index

An FM-Index is a compressed full-text substring index based on suffix arrays, bit vectors, wavelet trees and the Burrows–Wheeler transform. It can be used to find the number of occurrences of a pattern without prior tokenization within the compressed text, as well as locate the position of each occurrence and extract (decompress) the matched strings or their vicinity. The query time and the required storage space have a sublinear complexity with respect to the size of the input data. It is used extensively in the world of bioinformatics.

Supported operations:

count enables to count the number of occurrences of a given pattern. This is extremely fast.
locate enables to find all the leftmost starting positions of a given pattern. Its speed will depend on the parameter sample rate which trades off space for speed. A sample rate of 4 means to store an additional integer every four input symbols but also means that up to 4 additional rank queries will be necessary per query. Therefore, more position integers require more space but reduce the number of searches.
extract enables extracting original input text from the compressed index between given positions. Its performance is also affected by the sample rate.
extractUntilBoundary enables extracting a window of the original text delimited by a boundary character (e.g., a record delimiter such as \n)

As of now, the FM-Index implementation supports up to 32,768 different UTF-8 encoded characters. So far it has been tested with data inputs of around ~400 MB, including general text documents, system logs, system traces, etc.

References:

Wikipedia
Ferragina, Paolo, and Giovanni Manzini. "Opportunistic data structures with applications." In Proceedings 41st annual symposium on foundations of computer science, pp. 390-398. IEEE, 2000.

Suffix arrays

A suffix array is a sorted array of all suffixes of an input string. It can be used as index to locate all occurrences of a given substring p by performing two binary searches per pattern. The drawback of a suffix array is its usually large size. The FM-Index, as described above, tackles some of its shortcomings.

The version used here is a modification of the JsuffixArray Repository which in turn is a port of the original divsufsort implementation (find it here)

Wikipedia
JsuffixArray repository

RRR Bit vectors

A bit vector is a string of bits, as the name indicates. Without supporting data structures, rank, select or access queries on the bit strings are very slow (e.g. O(n)). The RRR bit vectors are a data structure built on top of the bit string that answers e.g. rank queries in nearly constant time while also compressing it with space requirements close to the zero-th entropy.

For further details see:

RRR bit vector tutorial
Raman, Rajeev, Venkatesh Raman, and Srinivasa Rao Satti. "Succinct indexable dictionaries with applications to encoding k-ary trees, prefix sums and multisets." ACM Transactions on Algorithms (TALG) 3, no. 4 (2007): 43-es.
Claude, Francisco, and Gonzalo Navarro. "Practical rank/select queries over arbitrary sequences." In International Symposium on String Processing and Information Retrieval, pp. 176-187. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008.

Wavelet trees / matrix / block-boosting

The Wavelet Tree is a succinct data structure to store strings in compressed space. It generalizes the rank, select and access operations defined on bit vectors to arbitrary alphabets. This means that you can perform queries on arbitrary symbols on an arbitrarily long string without requiring to keep the whole string in memory. An example rank query is "how many times does the symbol c appear in string s between positions p1 and p2". With the combination of RRR bit vectors, the wavelet tree can answer e.g. rank queries in O(log2 |A|), where A is the alphabet used in the input string.

Note that here the implementation used is the fixed-block boosting wavelet tree which is based on the clever idea that because we represent the Burrows-Wheeler transform (and not the input corpus itself), it is actually better to build multiple wavelet trees over the transform. These are called blocks, and because characters in the transform are more likely to be adjacent to each other (creating the so-called "BW-Runs"), the alphabet is usually smaller as well, therefore requiring less levels in the tree to represent the transform.

Supported operations:

rank enables to count the number of occurrences of a symbol c between positions p1 and p2 in logarithmic time (as opposed to naive O(p2-p1) which grows linearly with the difference of positions).
access enables to retrieve the symbol at position p. Remember that the wavelet tree does not store the original input string.
select answers at which position is the i-th appearance of symbol c.

References:

Gog, Simon, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, and Simon J. Puglisi. "Faster, minuter." In 2016 Data Compression Conference (DCC), pp. 53-62. IEEE, 2016.
Gog, Simon, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, and Simon J. Puglisi. "Fixed block compression boosting in FM-indexes: Theory and practice." Algorithmica 81 (2019): 1370-1391.
Original implementation by Dominik Kempa

Burrows-Wheeler transform

The Burrows-Wheeler transform is a rearrangement of an input string into runs of similar characters. For example, the word ^BANANA$ would be rearranged into BNN^AA$A, where two Ns and As are adjacent. In the case of longer strings, this usually means compression can be applied, therefore making it a lossless compression algorithm. Because of its relation to the Suffix array via the LF-Mapping, it is very useful for the FM-Index as a way of navigating a suffix array without requiring to store all suffixes. It can also be used as a measure of the compressibility or redundancy of a string.

References

Wikipedia
Manzini, Giovanni. "An analysis of the Burrows—Wheeler transform." Journal of the ACM (JACM) 48, no. 3 (2001): 407-430.

About this project

Please note that this product is not officially supported by Dynatrace.

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index4j

Content

First steps

Supported data structures

How-to

Using the FM-Index

Creating an FM-Index

Counting occurrences of a pattern

Locating the positions of an occurrence

Extracting key-value pairs

Extracting whole records

Serializing

Using RRR Bit vectors

Creating RRR Bit vectors

Ranking zeros or ones

Access an arbitrary position

Serializing

Using Wavelet trees

Creating FBB-WT

Ranking symbols

Accessing symbols

Serializing

Benchmarks

Infrastructure

Trade off plots between speed and space

Locate queries

Extract/decompress queries

Compression evaluation

Index construction runtime

Details

FM-Index

Suffix arrays

RRR Bit vectors

Wavelet trees / matrix / block-boosting

Burrows-Wheeler transform

About this project