Cedar implements an updatable double-array trie [1,2,3], which offers fast update/lookup for skewed queries in real-world data, e.g., counting words in text or mining conjunctive features in a classifier. Its update and lookup speed is comparable to (hard-to-serialize) hash-based containers (std::unordered_map) or modern cache-conscious tries [3,4] and even faster when the queries are short and skewed (see performance comparison).
The cedar is meant for those who still underestimate a double-array trie as a mutable container. The double-array tries are no longer slow to update. It's actually fast.
If you make use of cedar for research or commercial purposes, the reference will be:
N. Yoshinaga and M. Kitsuregawa. A Self-adaptive Classifier for Efficient Text-stream Processing. Proc. COLING 2014, pp. 1091--1102. 2014.
std::unordered_map, while the random insertion is comparable.std::unordered_map, while the random lookup is comparable.NaN values for float record. You can of course associate a five- or more byte record with a key by preparing a value array and store its index (int) in the trie.std::map unless a user sets the third template parameter SORT_KEYS to false (slightly faster update).#define USE_REDUCED_TRIE 1 before #include <cedar.h>, while a minimal-prefix trie is enabled if you #include <cedarpp.h> instead of cedar.h.#include <cedarpp.h>) when you wonder which trie to use for your datasets or benchmark experiments with various kinds of keys. Only when the keys are short, use a normal trie (#include <cedar.h>). Use the reduced trie (#include <cedar.h> preceded by #include USE_REDUCED_TRIE) cautiously since it has some limitations on the values as stated above. The normal trie and the reduced trie are not meant for long keys.License: GNU GPLv2, LGPLv2.1, and BSD; or e-mail me for other licenses you want.
> wget http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/cedar/cedar-latest.tar.gz
> tar zxvf cedar-latest.tar.gz
> cd cedar-YYYY-MM-DD
> configure
> make installshrink_to_fit()).set_array() in cedarpp.h (thanks to GK)begin() and next() to realize iterater-based (sorted) key traversal (depth-first search).predict() and dump() using begin() and next(); faster retrieval in tries other than double-array prefix trie (cedarpp.h).dump() for a trie loaded from file.erase() (-1 if absent).cedarpp.h)configure --enable-prefix-trie to compile cedar/mkcedar with cedarpp.h.#include <cedarpp.h> if you want to use this minimal-prefix trie in your code.shrink_tail() removes unused elements in TAIL (automatically evoked in saving a trie if you set the (additional) third parameter of save() to true).update(), you may need to use cedar::npos_t instead of size_t.configure --enable-reduced-trie to compile cedar/mkcedar with this optimization.#define USE_REDUCED_TRIE prior to #include <cedar.h> if you want to use this reduced trie in your code.int record r (0 ≤ r < 231 - 1).MAX_TRIAL is now in default set to 1 (formerly, 8).#include <stdint.h> to improve portability.update() had destroyed (BASE of the root of) the trie).
update() rejects an empty string.erase() skips an empty string.exactMatchSearch() returns false for an empty string.commonPrefixPredict() returns 0 for an empty string.update() and predict() from an immutable trie (configure --enable-fast-load will save/load the extra data to directly save/load a mutable trie.)#define USE_EXACT_FIT prior to #include <cedar.h>.std::realloc().total_size() that returns memory consumed by the double array.commonPrefixPredict() to enumerate keys from given prefix.SORTED_KEYS is false.Cedar provides the following class template:
template <typename value_type,
const int NO_VALUE = nan <value_type>::N1,
const int NO_PATH = nan <value_type>::N2,
const bool ORDERED = true,
const int MAX_TRIAL = 1,
const size_t NUM_TRACKING_NODES = 0>
class da;This declares a double array trie with value_type as record type; NO_VALUE and NO_PATH are error codes returned by exactMatchSearch() or traverse() if search fails due to no path or no value, respectively. The keys in a trie is sorted if ORDERED is set to true, otherwise siblings are stored in an inserted order (slightly faster update). MAX_TRIAL is used to control space and time in online trie construction (useful when you want to build a trie from binary keys). If NUM_TRACKING_NODES is set to a positive integer value, the trie keeps node IDs stored in its public data member tracking_node to be valid, even if update() relocates the nodes to different locations.
The default NO_VALUE/NO_PATH values for int record are -1 and -2 (same as darts-variants), while the values for float record are 0x7f800001 and 0x7f800002 (taken from NaN values in IEEE 754 single-precision binary floating-point format); they can be referred to by CEDAR_NO_VALUE and CEDAR_NO_PATH, respectively.
NOTE: value_type must be in less than or equal to four (or precisely sizeof (int)) bytes. This does not mean you cannot associate a key with a value in five or more bytes (e.g., int64_t, double or user-defined struct). You can associate any record with a key by preparing a value array by yourself and store its index in (int) the trie (cedar::da <int>).
Cedar supports legacy trie APIs adopted in darts-clone, while providing new APIs for updating a trie.
value_type& update (const char* key, size_t len = 0, value_type val = value_type (0))key with length = len and value = val. If len is not given, std::strlen() is used to get the length of key. If key has been already present int the trie, val is added to the current value by using operator+=. When you want to override the value, omit val and write a value onto the reference to the value returned by the function.int erase (const char* key, size_t len = 0, size_t from = 0)key (suffix) of length = len at from (root node in default) in the trie if exists. If len is not given, std::strlen() is used to get the length of key. erase() returns -1 if the trie does not include the given key. Currently, erase() does not try to refill the resulting empty elements with the tail elements for compaction.template <typename T>
size_t commonPrefixPredict (const char* key, T* result, size_t result_len, size_t len = 0, size_t from = 0)key of length = len from a node at from, and stores at most result_len elements in result. result must be allocated with enough memory by a user. To recover keys, supply result in type cedar::result_triple_type (members are value, length, and id) and supply id and length to the following function, suffix(). The function returns the total number of suffixes (including those not stored in result).template <typename T>
void dump (T* result, const size_t result_len)suffix() to obtain actual key strings (this function works as commonPrefixPredict() from the root). To get all the results, result must be allocated with enough memory (result_len = num_keys()) by a user.begin() and next(), which enumerate the leaf nodes of a given tree by a pre-order walk; to predict one key by one, use these functions directly.int begin (size_t& from, size_t& len)from and return a value associated with the first (left-most) leaf node of the subtree. If the trie has no leaf node, it returns CEDAR_NO_PATH. Upon successful completion, from will point to the leaf node, while len will be the depth of the node. If you specify some internal node of a trie as from (in other words from != 0), remember to specify the depth of that node in the trie as len.int next (size_t& from, size_t& len, const size_t root = 0)root from a leaf node of depth len at from and return a value of the next (right) leaf node. If there is no leaf node at right-hand side of the subtree, it returns CEDAR_NO_PATH. Upon successful completion, from will point to the next leaf node, while len will be the depth of the node. This function is assumed to be called after calling begin() or next().void suffix (char* key, const size_t len, size_t to)key of length = len in a trie that reaches node to. key must be allocated with enough memory by a user (to store a terminal character, len + 1 bytes are needed). Users may want to call some node-search function to obtain a valid node address and the (maximum) value of the length of the suffix.void restore()predict(), dump() and update() are on-demand recovered when the function executed. This will incur some overhead (at the first execution). To avoid this, a user can explicitly run restore() just after loading the trie. This command is not defined when you configure --enable-fast-load since the configuration allows you to directly save/load a mutable double array.There are three major updates to the legacy APIs.
build() accepts unsorted keys.exactMatchSearch() returns CEDAR_NO_VALUE if search fails.traverse() returns CEDAR_NO_VALUE if the key is present as prefix in the trie (but no value is associated), while it returns CEDAR_NO_PATH if the key is not present even as prefix.update() can relocate the node id (from) obtained by traverse(), a user is advised to store the traversed node IDs in public data member tracking_node so that cedar can keep the IDs updated. The maximum number of elements in tracking_node should be specified as the sixth template parameter (0 is used as a sentinel).We compared cedar (2014-06-24) with the following in-memory and mutable containers that support sequential insertions.
gcc-7.1): hash tableThese containers do not support serialization. We also compared cedar with the trie implementations that support serializations; the softwares other than cedar implement only static or immutable data structures that do not support update.
The succinct tries (*) do not store records; it needs extra space to store records (sizeof (int) * #keys bytes) and additional time to lookup it.
Unless otherwise versions are stated, codes in the latest snapshots of git or svn repository were used.
Having a set of keys and a set of query strings, we first build a container that maps a key to a unique value, and then look up the queries to the container. The codes used to benchmark containers (bench.cc and bench_static.cc) have been updated from the ones included in the latest cedar package. The slow-to-build or slow-to-lookup comparison-based containers and immutable double arrays are excluded from the benchmark (the previous results are still available from here). The entire keys (and queries) are loaded into memory to exclude I/O overheads before insertion (and look-up). All the hash-based containers use const char* in stead of expensive std::string to miminize the memory footprint and to exclude any overheads, and adopt CityHash64 from Google's cityhash in stead of default hash functions for a fair comparison. To compute the maximum memory footprint required in inserting the keys into the data structures, we subtracted the memory usage after loading keys or queries into memory from the maximum memory usage of the process monitored by run.cc (for mac) (or run_linux.cc).
Since we are interested in the lookup performance for practical situations where a small number of frequent keys are queried significantly more than a large number of rare ones (Zipfian distribution), the following datasets are used for experiments.
The statistics of keyset are summarized as follow (a terminal symbol included):
| Keyset | Text | Binary |
|---|---|---|
| Size [bytes] | 304,562,809 | 144,703,811 |
| Size (prefix) [bytes] | 263,848,821 | 144,417,733 |
| Size (tail) [bytes] | 51,932,403 | 570,117 |
| # keys | 28,772,169 | 26,194,354 |
| Ave. length [bytes] | 10.58 | 5.52 |
| Ave. length (prefix) [bytes] | 9.17 | 5.51 |
| Ave. length (tail) [bytes] | 1.80 | 0.02 |
| # nodes in trie | 78,252,617 | 26,725,019 |
| # nodes in trie (prefix) | 37,538,629 | 26,439,275 |
From these statistics, we can compute the minimum size of double-array trie (cedar). It requires 8 * #nodes for internal nodes plus 8 * #keys for additional terminals that store 4-byte records. Concretely speaking, cedar requires at least 816.53 MiB (78,252,617 * 8 + 28,772,169 * 8 = 856,198,288) for text keyset, while it requires at least 403.74 MiB (26,725,019 * 8 + 26,194,354 * 8 = 423,354,984 bytes) for binary keyset.
Similarly, if a container stores raw keys and values, it requires at least 400.21MiB (304,562,809 + 4 * 28,772,169 = 419,651,485 bytes) for text keyset while it requires 237.92MiB (144,703,811 + 4 * 26,194,354 = 249,481,227) for binary keyset. Remember that a pointer (or offset) variable is additionally needed to access variable-length keys, while the memory alignment (e.g., 16 bytes in Mac OS X) incur severe overheads for short-length keys (if they are memory-allocated individually). If naively adopting std::string in hash-based containers, its space overheads are substantial (cf. previous resuls using std::string)
The statistics of queryset are summarized as follow (a terminal symbol included):
| Queryset | Text | Binary |
|---|---|---|
| Size [bytes] | 1,079,467,570 | 915,918,218 |
| # queries | 177,999,203 | 216,784,450 |
| # keys | 612,219 | 16,839,036 |
| Ave. length [bytes] | 6.06 | 4.23 |
| Ave. key count | 290.74 | 12.87 |
For the in-memory containers we measured the insertion and the lookup time per key. For the (static) tries we measured time to build the trie from the keyset (including time needed to save the trie into a hard disk; we alphabetically sort the keys in advance since some (static) tries require the sorted keys as input) and the lookup time per key.
The experiments were conducted on Mac OS X 10.11 over Intel Core i7-3720QM 2.6Ghz CPU with 16GB main memory. The benchmark codes are compiled for each container with gcc-7.1 -O2 -g -std=c++17. The best of five consective trials has been reported for each container.
The following table lists the timings needed in inserting keys (Insert), looking up the keys (Lookup), and maximum resident set size (memory) occupied by the process in inserting a trie (Space). Click the tabel headings for sorting.
| Software | Data Structure | Space [MiB] | Insert [ns/key] | Lookup [ns/key] |
|---|---|---|---|---|
| cedar | Double-array trie | 1171.74 | 651.47 | 54.59 |
cedar ORDERED=false | Double-array trie | 1173.05 | 638.62 | 53.98 |
| cedar | Double-array reduced trie | 961.65 | 656.25 | 56.78 |
cedar ORDERED=false | Double-array reduced trie | 961.55 | 635.98 | 56.49 |
| cedar | Double-array prefix trie | 680.63 | 845.29 | 52.35 |
cedar ORDERED=false | Double-array prefix trie | 678.29 | 817.85 | 53.95 |
| Judy 1.0.5 | Judy trie SL | 928.95 | 764.22 | 188.75 |
| hat-trie | HAT-trie | 570.00 | 620.40 | 64.27 |
| Array hash | Array Hash | 1575.01 | 691.87 | 37.85 |
| Hopscotch hash | Hopscotch Hash | 1581.38 | 395.80 | 48.25 |
| sparsepp | Hash table (sparse) | 1104.29 | 686.62 | 67.74 |
| sparsetable 2.0.2 (dense) | Hash table (dense) | 1941.53 | 372.65 | 43.74 |
| std::unordered_map | Hash table | 1843.65 | 546.84 | 103.38 |
| log | log | |||
The following table lists the timings needed in building a trie from sorted keyset (Build), looking up the keys (Lookup), maximum resident set size (memory) occupied by the process in inserting a trie (Space), and the size of trie saved in hard disk (Size).
| Software | Data Structure | Space [MiB] | Size [MiB] | Build [ns/key] | Lookup [ns/key] |
|---|---|---|---|---|---|
| cedar | Double-array trie | 1006.57 | 816.54 | 205.39 | 42.95 |
cedar ORDERED=false | Double-array trie | 1006.57 | 816.54 | 182.35 | 42.23 |
| cedar | Double-array reduced trie | 781.30 | 642.38 | 188.00 | 44.58 |
cedar ORDERED=false | Double-array reduced trie | 787.31 | 642.38 | 178.22 | 44.38 |
| cedar | Double-array prefix trie | 489.49 | 488.38 | 214.58 | 39.98 |
cedar ORDERED=false | Double-array prefix trie | 489.48 | 488.35 | 204.29 | 40.96 |
| Darts 0.32 | Double-array trie | 4305.09 | 858.93 | 2522.85 | 40.54 |
| Darts-clone 0.32g | Directed-acyclic word graph | 2310.43 | 409.17 | 1359.94 | 34.55 |
| Darts-clone 0.32e5 | Compacted double-array trie | 2778.06 | 309.31 | 1033.19 | 59.12 |
| tx-trie 0.18 | LOUDS trie | 1345.68 | *113.11 | 603.93 | 944.18 |
| ux-trie 0.1.9 | LOUDS two-trie | 1729.32 | *92.39 | 848.49 | 2059.98 |
| marisa-trie 0.2.4 | LOUDS nested patricia trie | 2034.10 | *87.27 | 682.64 | 190.12 |
| log | log | ||||
* The succinct tries need additional space for record: 28,772,169 * sizeof (int) = 109.76 MiB (115,088,676 bytes).
The following table lists the timings needed in inserting keys (Insert), looking up the keys (Lookup), and maximum resident set size (memory) occupied by the process in inserting a trie (Space).
| Software | Data Structure | Space [MiB] | Insert [ns/key] | Lookup [ns/key] |
|---|---|---|---|---|
| cedar | Double-array trie | 569.63 | 188.90 | 12.08 |
cedar ORDERED=false | Double-array trie | 539.02 | 155.40 | 12.17 |
| cedar | Double-array reduced trie | 494.02 | 204.94 | 8.15 |
cedar ORDERED=false | Double-array reduced trie | 495.35 | 172.47 | 8.08 |
| cedar | Double-array prefix trie | 537.62 | 224.46 | 9.72 |
cedar ORDERED=false | Double-array prefix trie | 539.35 | 190.07 | 9.67 |
| Judy 1.0.5 | Judy trie SL | 562.99 | 231.46 | 81.51 |
| hat-trie | HAT-trie | 449.61 | 223.02 | 50.09 |
| Array hash | Array Hash | 1395.09 | 642.51 | 75.27 |
| Hopscotch hash | Hopscotch Hash | 1568.71 | 395.42 | 61.19 |
| sparsepp | Hash table (sparse) | 982.46 | 700.29 | 109.09 |
| sparsetable 2.0.2 (dense) | Hash table (dense) | 1924.07 | 370.93 | 67.52 |
| std::unordered_map | Hash table | 1685.14 | 542.04 | 212.21 |
| log | log | |||
The following table lists the timings needed in building a trie from sorted keyset (Build), looking up the keys (Lookup), maximum resident set size (memory) occupied by the process in inserting a trie (Space), and the size of trie saved in hard disk (Size).
| Software | Data Structure | Space [MiB] | Size [MiB] | Build [ns/key] | Lookup [ns/key] |
|---|---|---|---|---|---|
| cedar | Double-array trie | 486.53 | 403.75 | 190.48 | 8.42 |
cedar ORDERED=false | Double-array trie | 486.73 | 403.75 | 162.69 | 8.66 |
| cedar | Double-array reduced trie | 441.57 | 368.14 | 206.56 | 7.60 |
cedar ORDERED=false | Double-array reduced trie | 443.65 | 369.80 | 173.49 | 7.31 |
| cedar | Double-array prefix trie | 514.73 | 484.64 | 232.12 | 8.16 |
cedar ORDERED=false | Double-array prefix trie | 516.20 | 486.42 | 193.07 | 8.22 |
| Darts 0.32 | Double-array trie | 1573.27 | 406.03 | 338.32 | 7.70 |
| Darts-clone 0.32g | Directed-acyclic word graph | 1618.92 | 201.91 | 657.87 | 8.32 |
| Darts-clone 0.32e5 | Compacted double-array trie | 2525.98 | 272.07 | 1180.55 | 15.43 |
| tx-trie 0.18 | LOUDS trie | 1228.44 | *38.63 | 372.62 | 298.06 |
| ux-trie 0.1.9 | LOUDS two-trie | 1152.00 | *38.23 | 322.44 | 1036.02 |
| marisa-trie 0.2.4 | LOUDS nested patricia trie | 1438.70 | *41.62 | 261.31 | 430.24 |
| log | log | ||||
* The succinct tries need additional space for record: 26,194,354 * sizeof (int) = 99.92 MiB (104,777,416 bytes).
Conclusions: Overall, the cedar variants are comparable to the cache-conscious or optimized hash containers in terms of speed to update. The cedar variants are also comparable to those containers in terms of speed to lookup on the text datasets (keys with low branching factors and longer tails) and are significantly faster on the binary datasets (keys with with high branching factors). Although the cedar variants require more space to de/serialize the resulting tries than the other immutable double-array or succinct tries, they require significantly smaller spaces in building a trie. The double-array tries are no longer slow to update. It's actually fast.
For those who want to use Jagger in prgoramming languages other than C++, the following third-party contributions to ports and bindings (wrappers) are available.
We do not guarantee that the implemented algorithms other than those proposed by us are patent-free; we regarded them to be patent-free simply because their implementations are available as (existing) open-source softwares (otherwise a simple patent lookup). Please be careful when you use this software for commercial use.
The library is named after cedar, the most popular kind of tree in Japan; so just pronounce the same as cedar in English.
This software cannot be implemented without help of Dr. Yata, guru of double-array / succinct tries. The developer deeply appreciates his guidance on the implementation of the mechanism that controls space and time [2].