HFTrie

A dynamic data structure for indexing 64-bit binary codes for efficient nearest neighbor search. The index offers the capability to add, delete and range search for all points within a given radius of a target point.

Description

The HFTrie is a data structure where the indexed elements - or data points - are treated as a sequence of bits. Each layer of the trie sorts the data points according to a prefix portion of bits. For example, layer one sorts the data point into a subnode corresponding to the value of its first bit. The second layer sorts the datapoints into the subnode for the value of its first two bits. And so on.

flowchart TD
		  root[R] --> L[0xxx]
		  root[R] --> R[1xxx]
		  L --> LL[00xx]
		  L --- RR[01xx]
		  R --> LL_[10xx]
		  R --> RR_[11xx]

That's the basic idea, but for efficiency, the bits are chunked together. So, instead of considering only one bit per level, multiple bits (e.g. 4) are used from the bit sequence at each level to sort into child nodes. This naturally increases the fanout of each node. For two bits per layer, each node will sort into four possible child nodes. For 4 bits per layer, there are 16 possible child nodes. And so on.

Performance

Here are the performance metrics for the HFTrie for various index sizes. The insert and query times are the average times it takes to insert or query the index. Query Operations is for the average number of distance calculations performed for a range search, normalized to the size of the index and expressed as a percentage. The last column is for the recall percentage, or the average proportion of the cluster that should be returned with each query. The fast range search sacrfices a bit in accuracy for a significant boost in speed efficiency.

Fast Range Search

N	MEM	Insert Time	Query Opers.	Query Time	Recall
100K	4.0MB	135 ns	0.97%	37.1 μs	87.2%
200K	6.5MB	146 ns	0.96%	72.9 μs	89.4%
400K	12MB	172 ns	0.89%	124 μs	88.2%
800K	35MB	241 ns	0.43%	206 μs	86.2%
1M	45MB	263 ns	0.34%	250 μs	86.0%
2M	75MB	297 ns	0.30%	387 μs	86.2%
4M	127MB	330 ns	0.30%	618 μs	85.6%
8M	268MB	373 ns	0.25%	953 μs	85.0%
16M	727MB	461 ns	0.11%	1.75 ms	85.2%
32M	1.2GB	538 ns	0.09%	3.27 ms	86.4%
64M	1.9GB	613 ns	0.09%	5.21 ms	86.4%
128M	4.3GB	674 ns	0.08%	7.39 ms	92.4%

For a constant index size, N = 4M, the query performance varies for different radius values. Better accuracy is guaranteed for lower radius searches with modest reductions in accuracy for larger range searches.

Radius	Query Opers.	Query Time	Recall
0	0.0003%	1.46 μs	100%
2	0.02%	49.0 μs	99.8%
4	0.02%	434 μs	96.6%
6	0.30%	613 μs	93.4%
8	0.30%	617 μs	88.6%
10	0.30%	616 μs	83.2%
12	0.30%	619 μs	88.8%

Standard Range Search

A standard range search guarantees query accuracy with significant added costs to speed.

N	MEM	Insert time	Query Opers.	Query Time	Recall
100K	4.0MB	134 ns	89.5%	3.40 ms	100%
200K	6.5MB	142 ns	89.5%	6.54 ms	100%
400K	12MB	169 ns	86.7%	11.7 ms	100%
800K	35MB	238 ns	65.7%	30.4 ms	100%
1M	45MB	257 ns	60.7%	39.7 ms	100%
2M	75MB	295 ns	58.8%	68.5 ms	100%
4M	127MB	327 ns	58.6%	111 ms	100%
8M	268MB	363 ns	51.2%	191 ms	100%
16M	727MB	457 ns	29.0%	454 ms	100%
32M	1.2GB	533 ns	27.1%	783 ms	100%
64M	1.9GB	604 ns	27.0%	1.29 s	100%
128M	4.3GB	665 ns	22.8%	1.95 s	100%

Comparison

Here is a comparison of different methods of indexing a uniform distributed data set of 4 million. Query operations notes the number of distance computations performed per query, normalized to the size of the dataset. All search queries are peformed for a radius = 10. Note that all methods underperform a simple sequential search at such a large radius. Only the HFTrie's fast range search outperforms the sequential search with the drawback that it is only able to achieve 85% recall of all cluster objects for an extended radius. It is, however, guaranteed to return all exact matches for smaller range searches.

For data set size, N = 4M and query radius = 10:

Method	MEM	Insert Time	Query Opers.	Query Time	Recall
SequentialSearch	64MB	n/a	100%	9.08 ms	100%
MVPTree	2.67GB	43.9μs	25.0%	276 ms	100%
MTree	113MB	631ns	69.5%	68.2 ms	100%
HWTree	312MB	1.69 μs	17.6%	222 ms	100%
HFTrie-std	124MB	327 ns	58.6%	111 ms	100%
HFTrie-fast	124MB	330 ns	0.30%	618 μs	85.6%

You can run these tests with the compiled program runhftrie. View the source in tests/run_hftrie.cpp.

Install

cmake .
make
make test
make install

Simple API

HFTrie trie;

long long id;
uint64_t code;

// insert an element
trie.Insert({ id, code });

// delete an element
trie.Delete({ id, code });


uint64_t target;
int radius = 10;
vector<hf_t> results trie.RangeSearch(target, radius);

size_t sz = trie.Size();

size_t nbytes = trie.MemoryUsage();

// for debugging
trie.Print(cout);