Java High-Performance Library for Lattices
Java
Switch branches/tags
Nothing to show
Clone or download

README.md

JHPL - Java High-Performance Library for Lattices

Background

In mathematics, a lattice is a partially ordered set L in which every two elements have a unique supremum (also called a least upper bound) and a unique infimum (also called a greatest lower bound). A bounded lattice is a lattice that additionally has a greatest element 1 and a least element 0, which satisfy 0 <= x <= 1 for every x in L. (Source: Wikipedia)

Lattices can be modeled with Hasse diagrams. In order theory, a Hasse diagram is a type of mathematical diagram used to represent a finite partially ordered set, in the form of a drawing of its transitive reduction. (Source: Wikipedia)

This library has been designed to model a specific type of bounded lattices, in which each element is a combination of elements from different dimensions. The elements from each dimension are required to have a total order. Natural numbers with a given number of digits are a good example. For example, all natural binary numbers with 2 digits form a lattice in which each dimension can have a value of either 0 or 1 (0 < 1). It can be visualized with the following diagram:

Level-2    (1,1)
           /   \
Level-1 (0,1) (1,0)
           \   /
Level-0    (0,0)

The aim of this library is to efficiently represent very large such lattices, while allowing information to be stored about individual elements and groups of elements as well as supporting the enumeration of elements with certain properties.

Motivation

The type of lattices modeled by this library can become very large. If a lattice consists of elements with n dimensions, where each dimension i with (0 <= i < n) has m_i different components, the total number of elements is m_0 * m_1 * ... * m_(n-1).

The aim of this library is to efficiently (in terms of space and time complexity) represent lattices by storing information about elements only implicitly. You may, for example, use this library if you have a search problem for which the solution space can be expressed as a lattice. JHPL supports lattices with up to 2^63-1 (~9.223372 * 10^18) elements and materialized information with up to (2^31-1)*4 / (1024^3) = 8 GiB of memory. Of course, having such large lattices only makes sense if you do not need to store information about all elements. In particular, JHPL supports the concept of predictive properties.

A predictive property is a property that is automatically inherited to all (direct and indirect) successors or (direct and indirect) predecessors of an element to which it has been assigned. With predictive properties, very large spaces can be classified without traversing each element and without explicitly storing information about all elements. JHPL supports properties that are inherited to all successors, to all predecessors, or to both successors and predecessors. Moreover, JHPL also acts a map which allows to associated objects with individual elements, if required.

Overview

JHPL supports lattices in which each dimension consists of a set of objects (optionally of a given type). For example, the following lattice represents binary numbers with two digits, where each digit is represented by a string:

// Elements per dimension
String[][] elements = new String[][]{ {"0", "1"}, 
                                      {"0", "1"}};
        
// Create lattice with String-keys and Integer-values 
// (the type of objects that may be assigned to individual elements)
Lattice<String, Integer> lattice = new Lattice<String, Integer>(elements); 

Spaces

Elements from lattices may be represented in three different spaces:

  • The source space: This space is meant to provide natural representations of elements, e.g., (A, B, C).
  • The id space: In this space, each element is represented by an identifier, which is a positive long value. You may use this representation to store larger sets of elements or to use them as keys in maps.
  • The index space: This space represents elements by indices that correspond to the position of each element in the source space. For example, the index representation of ("0", "1") is (0, 1). All interactions with this library are performed in the index space.

Methods for converting between the different spaces are encapsulated in a class that is accessible via the method lattice.space(). Some examples:

// Example element
String[] element = new String[]{"0", "1"};

// Convert source to id 
long id = lattice.space().toId(element);

// Convert source to index
int[] index = lattice.space().toIndex(element);

// Convert index to source
element = lattice.space().toSource(index);

Additionally, the class provides methods for converting iterators:

  • Iterator<Long> indexIteratorToIdIterator(Iterator<int[]>)
  • Iterator<T[]> indexIteratorToSourceIterator(Iterator<int[]>)
  • Iterator<int[]> idIteratorToIndexIterator(Iterator<Long>)
  • Iterator<T[]> idIteratorToSourceIterator(Iterator<Long>)
  • Iterator<int[]> sourceIteratorToIndexIterator(Iterator<T[]>)
  • Iterator<Long> sourceIteratorToIdIterator(Iterator<T[]>)

Nodes

Methods for working with nodes are encapsulated in a class that is accessible via the method lattice.nodes(). Some examples:

// Top and bottom elements
int[] top = lattice.nodes().getTop();
int[] bottom = lattice.nodes().getBottom();

// Iterate over neighbors
Iterator<int[]> successors = lattice.nodes().listSuccessors(bottom);

// Check relationships
boolean direct = lattices.nodes().isDirectParentChild(bottom, top);

Note: Never assume that the integer arrays returned by this library are newly allocated! Never manipulate them and don't store any references to them. If you need to keep track of a set of elements: use the id space. You may use efficient implementations of collections of primitive values, as, e.g., provided by the HPPC project. Example:

// List all successors of the bottom element
Iterator<int[]> iter = lattice.nodes().listSuccessors(lattice.nodes().getBottom());

// Store references
LongArrayList list = new LongArrayList();
while (iter.hasNext()) {
	list.add(lattice.space().toId(iter.next()));
}

// Work with the elements from the list
for (long e : list) {
	int[] index = lattice.space().toIndex(e);
	boolean stored = lattice.contains(index);
}

For your convenience, JHPL also contains a builder for elements from the source space:

int[] element = lattice.nodes().build().next("B").next("B").next("C").create();

Storing data

You may use this library to assign data or predictive properties to elements. Predictive properties are implemented in an according class and may have an optional label.

// Associated to an element and all direct and indirect successors
PredictiveProperty property1 = new PredictiveProperty(Direction.UP);

// Associated to an element and all direct and indirect predecessors
PredictiveProperty property2 = new PredictiveProperty(Direction.DOWN);

// Associated to an element and all direct and indirect successors and predecessors
PredictiveProperty property3 = new PredictiveProperty(Direction.BOTH);

The methods provided by the class Lattice are optimized for read access and have the following run-time complexities:

  • getData(node): Retrieves the associated data. Guaranteed O(1).
  • putData(node, data): Associates data with a node. Guaranteed O(1).
  • contains(node): Returns whether any data is stored about a node. Guaranteed O(1).
  • hasProperty(node): Returns whether any property is associated with a node (includes inherited properties). The worst-case run-time complexity of this operation is O(#nodes for which put has been called with any property).
  • hasProperty(node, property): Determines whether a node is associated with a property (includes inherited properties). The worst-case run-time complexity of this operation is O(#nodes for which put has already been called with this property).
  • putProperty(node, property): Associates a node and predecessors or successors with a (predictive) property. The worst-case run-time complexity of this operation is O(#nodes for which put has already been called with this property).

Enumerating elements

JHPL provides two different ways of access to elements. Firstly, it allows accessing elements about which information has been explicitly stored (i.e. for which putData() or putProperty() has been called). These methods are safe to call at any time:

  • listNodes(): Enumerates all nodes stored in the lattice
  • listNodes(level): Enumerates all nodes stored on the given level

Secondly, JHPL also provides methods for accessing elements about which only implicit information is available. These methods are encapsulated in an object that is accessible via the method lattice.unsafe(). These methods may not be safe to call because their worst-case complexity is bound by the total number of nodes in the lattice. You should therefore only call them for "small" lattices (e.g., with up to a few million elements):

  • listAllNodes(): List all nodes in the lattice.
  • listNodesNotStored(): List all nodes for which no data is stored in the lattice.
  • listNodesWithProperty(): Lists all nodes which are associated with a property (includes inherited properties).
  • listNodesWithProperty(property): Lists all nodes which are associated with the given property (includes inherited properties).
  • listNodesWithPropertyOrStored(): Lists all nodes which are associated with a property (includes inherited properties) or for which data is stored.
  • listNodesWithoutProperty(): Lists all nodes which are not associated with any property (includes inherited properties).
  • listNodesWithoutProperty(property): Lists all nodes which are not associated with the given property (includes inherited properties).
  • listNodesWithoutPropertyAndNotStored(): Lists all nodes which are not associated with any property (includes inherited properties) and for which not data is stored.

Note: All of these methods support an optional parameter with which the level of the nodes that are to be returned may be specified.

Note: Similar methods are also provided for listing successors and predecessors with certain conditions (e.g. lattice.nodes().listSuccessorsWithoutProperty(node)). These are safe to call at any time.

Note: Never assume that the integer arrays returned by this library are newly allocated! Never manipulate them and don't store any references to them. If you need to keep track of a set of elements: use the id space.

Note: Methods from this library do not support concurrent modifications. An according exception will be raised.

Note: Methods from this library are not thread-safe.

Details and Evaluation

How it works

JHPL uses tries to store implicit information about the contained elements. It manages one trie per property (and direction) as well as a "master" trie for all elements. The tries use the index representation of the components of an element and they are serialized into integer arrays. When checking whether a given element has a certain property, the according trie is traversed while comparing elements with greater-than-or-equals for properties that are inherited to predecessors or with less-than-or-equals for properties that are inherited to successors. This scheme works, as long as the following two conditions are met:

  1. It is made sure that no properties are stored for elements that already have the given property. Counterexample:
  • Assume property A is predictive in an upwards direction.
  • We first add property A for (1, 2, 1)
  • We then add property A for (1, 3, 25).
  • We query for (1, 3, 20) with <= and the result will be false (which is wrong).
  1. It is made sure that all obsolete properties are removed. Counterexample:
  • Assume property A is predictive in an upwards direction.
  • We first add property A for (1, 3, 25)
  • We then add property A for (1, 2, 1).
  • We query for (1, 3, 20) with <= and the result will be false (which is wrong).

The following output shows the in-memory representation of a lattice over the dimensions ({0, 1, 2, 3}, {0, 1}, {0, 1, 2}) for which put has been called with an upwards-predictive property for nodes (1, 1, 2) and (0, 0, 0):

Lattice
+---- Upwards-predictive properties
|   +---- Property1
|       +---- Trie
|           +---- Memory statistics
|           |   +---- Allocated: 76 [bytes]
|           |   +---- Used: 36 [bytes]
|           |   +---- Relative: 47.36842 [%]
|           +---- Buffer
|           |   +---- [9, 0, 0, 0, 0, 0, 0, 0, 0, 11, 0, -1, 0, 0, 0, 0, 0, 0, 0]
|           +---- Tree
|               +---- [0]
|               |     +---- [0]
|               |         +---- [0]
|               +---- [EOT]
+---- Master
|   +---- Trie
|       +---- Memory statistics
|       |   +---- Allocated: 76 [bytes]
|       |   +---- Used: 56 [bytes]
|       |   +---- Relative: 73.68421 [%]
|       +---- Buffer
|       |   +---- [9, 4, 0, 0, 0, 6, 0, 0, -1, 11, 0, -1, 0, 0, 0, 0, 0, 0, 0]
|       +---- Tree
|           +---- [0]
|           |     +---- [0]
|           |     │   +---- [0]
|           +---- [1]
|           |     +---- [1]
|           |         +---- [2]
|           +---- [EOT]
+---- Memory: 424 [bytes]

The difference in byte sizes (152 bytes for both tries vs. 424 bytes for the overall structure) is due to an additional hash table that may be used for associating data to elements.

Some numbers

Measured with a Lenovo Thinkpad T440s on Ubuntu 14.04 with an Oracle JVM 1.7.0 (rev. 72)

Space complexity

The following table shows a comparison of the in-memory size of lattices with 10^1 (ten) to 10^7 (ten million) elements. Each lattice has between 1 and 7 dimensions with 10 elements per dimension. The lattices have been materialized with a call to lattice.unsafe().materialize() which is a shortcut for calling putData() on all elements in the lattice.

#Elements Size Time Naive size
10^1=10 324 B 0 ms 1.1 kB
10^2=100 836 B 0 ms 13.3 kB
10^3=1000 6.7 kB 1 ms 151.2 kB
10^4=10000 48.8 kB 3 ms 1.7 MB
10^5=100000 533.3 kB 5 ms 18.8 MB
10^6=1000000 6.3 MB 35 ms 206.4 MB
10^7=10000000 47.8 MB 300 ms 2.2 GB

For reference, I included the expected in-memory size of a naive implementation, which maintains one integer-array representing components as well as pointers to successors and predecessors for each element.

Run-time complexity

Storing predictive properties

The following numbers show the time needed to assign a predictive property to all nodes of a lattice with 1 million elements (1 million calls to putProperty()). The best-case performance simply needs to check whether the property already exists and the worst-case performance needs to check, clear the trie and set the property.

  • Best-case: 236 milliseconds (236 nanoseconds per put-operation)
  • Worst-case: 647 milliseconds (647 nanoseconds per put-operation)
Enumerating elements

The following numbers show the time needed to enumerate all elements from a materialized lattice with 1 million elements.

1. Enumerating the elements level by level (in a natural order)
for (int level=0; level<lattice.numLevels(); level++) {
	processAll(lattice.listNodes(level));
}

This requires ~200ms with a maximum of 8 ms per level (55 levels in total).

2. Enumerating all elements (in a natural order)
processAll(lattice.listNodes());

This requires ~25ms.

Putting properties and enumerating elements

This is a more complex experiment. First, we create a lattice with 1 million elements. When then create five predictive properties, two of which are inherited to successors, two of which are inherited to predecessors and one of which is inherited to successors and predecessors.

1. Setting the properties

We associate each property to 10.000 random elements (50.000 put operations). This takes ~178 ms. The resulting lattice consumes about 3.2 MB of space.

2. Listing all nodes with any property level-by-level

For each level, we enumerate over all elements that are associated with any property. Additionally, we perform a space mapping by calling toId(element) for all elements returned by the iterators. This requires ~318 ms and returns 1M elements, meaning that all elements in the lattice are associated with at least one property as a result from step 1:

for (int level = 0; level < lattice.numLevels(); level++) {
	Iterator<int[]> iter = lattice.unsafe().listNodesWithProperty(level);
	processAll(lattice.space().indexIteratorToIdIterator(iter));
}

Calling listNodesWithoutProperty() exhibits comparable performance.

3. Listing nodes with a specific property level-by-level

For each level and each property, we enumerate over all elements that are associated with the property. Additionally, we perform a space mapping by calling toId(element) for all elements returned by the iterators. This requires ~3614 ms and returns 4.880.679 elements, meaning that on average, each element is associated with 4.9 properties:

for (PredictiveProperty property : properties) { 
	for (int level = 0; level < lattice.numLevels(); level++) {
	Iterator<int[]> iter = lattice.unsafe().listNodesWithProperty(level, property);
		processAll(lattice.space().indexIteratorToIdIterator(iter));
	}
}
4. Listing all nodes without any property

Again we also perform space mapping:

Iterator<int[]> iter = lattice.unsafe().listNodesWithoutProperty();
processAll(lattice.space().indexIteratorToIdIterator(iter));

This takes ~170 ms, compared to the 332 ms required for enumerating the elements level-by-level.

Download

A binary version (JAR file) is available for download here.

The according Javadoc is available for download here.

Documentation

Online documentation can be found here.

License

Apache 2.0