Merge pull request #56 from SymbolicML/MilesCranmer/issue14

Graph-like expressions

Author: MilesCranmer

Project.toml

@@ -1,7 +1,7 @@
 name = "DynamicExpressions"
 uuid = "a40a106e-89c9-4ca8-8020-a735e8728b6b"
 authors = ["MilesCranmer <[email protected]>"]
-version = "0.13.1"
+version = "0.14.0"
 
 [deps]
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
@@ -24,6 +24,7 @@ DynamicExpressionsSymbolicUtilsExt = "SymbolicUtils"
 DynamicExpressionsZygoteExt = "Zygote"
 
 [compat]
+Aqua = "0.7"
 Compat = "3.37, 4"
 LoopVectorization = "0.12"
 MacroTools = "0.4, 0.5"

benchmark/benchmarks.jl

@@ -1,6 +1,11 @@
 using DynamicExpressions, BenchmarkTools, Random
 using DynamicExpressions.EquationUtilsModule: is_constant
 using Zygote
+if PACKAGE_VERSION < v"0.14.0"
+    @eval using DynamicExpressions: Node as GraphNode
+else
+    @eval using DynamicExpressions: GraphNode
+end
 
 include("benchmark_utils.jl")
 
@@ -66,13 +71,15 @@ end
 
 # These macros make the benchmarks work on older versions:
 #! format: off
-@generated function _convert(::Type{N}, t; preserve_sharing) where {N<:Node}
+@generated function _convert(::Type{N}, t; preserve_sharing) where {N}
     PACKAGE_VERSION < v"0.7.0" && return :(convert(N, t))
-    return :(convert(N, t; preserve_sharing=preserve_sharing))
+    PACKAGE_VERSION < v"0.14.0" && return :(convert(N, t; preserve_sharing=preserve_sharing))
+    return :(convert(N, t))  # Assume type used to infer sharing
 end
 @generated function _copy_node(t; preserve_sharing)
     PACKAGE_VERSION < v"0.7.0" && return :(copy_node(t; preserve_topology=preserve_sharing))
-    return :(copy_node(t; preserve_sharing=preserve_sharing))
+    PACKAGE_VERSION < v"0.14.0" && return :(copy_node(t; preserve_sharing=preserve_sharing))
+    return :(copy_node(t))  # Assume type used to infer sharing
 end
 @generated function get_set_constants!(tree)
     !(@isdefined set_constants!) && return :(set_constants(tree, get_constants(tree)))
@@ -101,13 +108,36 @@ function benchmark_utilities()
         :index_constants,
         :string_tree,
     )
+    has_both_modes = [:copy, :convert]
+    if PACKAGE_VERSION >= v"0.14.0"
+        append!(
+            has_both_modes,
+            [
+                :simplify_tree,
+                :count_nodes,
+                :count_constants,
+                :get_set_constants!,
+                :index_constants,
+                :string_tree,
+            ],
+        )
+    end
 
     operators = OperatorEnum(; binary_operators=[+, -, /, *], unary_operators=[cos, exp])
     for func_k in all_funcs
         suite[func_k] = let s = BenchmarkGroup()
-            for k in (:break_sharing, :preserve_sharing)
-                has_both_modes = func_k in (:copy, :convert)
-                k == :preserve_sharing && !has_both_modes && continue
+            for k in (
+                if func_k in has_both_modes
+                    [:break_sharing, :preserve_sharing]
+                else
+                    [:break_sharing]
+                end
+            )
+                preprocess = if k == :preserve_sharing && PACKAGE_VERSION >= v"0.14.0"
+                    tree -> GraphNode(tree)
+                else
+                    identity
+                end
 
                 f = if func_k == :copy
                     tree -> _copy_node(tree; preserve_sharing=(k == :preserve_sharing))
@@ -132,12 +162,9 @@ function benchmark_utilities()
                     setup=(
                         ntrees=100;
                         n=20;
-                        trees=[gen_random_tree_fixed_size(n, $operators, 5, Float32) for _ in 1:ntrees]
+                        trees=[$preprocess(gen_random_tree_fixed_size(n, $operators, 5, Float32)) for _ in 1:ntrees]
                     )
                 )
-                if !has_both_modes
-                    s = s[k]
-                end
                 #! format: on
             end
             s

docs/src/types.md

@@ -48,16 +48,7 @@ Equations are specified as binary trees with the `Node` type, defined
 as follows:
 
 ```@docs
-Node{T}
-```
-
-There are a variety of constructors for `Node` objects, including:
-
-```@docs
-Node(::Type{T}; val=nothing, feature::Integer=nothing) where {T}
-Node(op::Integer, l::Node)
-Node(op::Integer, l::Node, r::Node)
-Node(var_string::String)
+Node
 ```
 
 When you create an `Options` object, the operators
@@ -69,23 +60,87 @@ When using these node constructors, types will automatically be promoted.
 You can convert the type of a node using `convert`:
 
 ```@docs
-convert(::Type{Node{T1}}, tree::Node{T2}) where {T1, T2}
+convert(::Type{AbstractExpressionNode{T1}}, tree::AbstractExpressionNode{T2}) where {T1, T2}
 ```
 
 You can set a `tree` (in-place) with `set_node!`:
 
 ```@docs
-set_node!(tree::Node{T}, new_tree::Node{T}) where {T}
+set_node!
 ```
 
 You can create a copy of a node with `copy_node`:
 
 ```@docs
-copy_node(tree::Node)
+copy_node
+```
+
+## Graph-Like Equations
+
+You can describe an equation as a *graph* rather than a tree
+by using the `GraphNode` type:
+
+```@docs
+GraphNode{T}
+```
+
+This makes it so you can have multiple parents for a given node,
+and share parts of an expression. For example:
+
+```julia
+julia> operators = OperatorEnum(;
+           binary_operators=[+, -, *], unary_operators=[cos, sin, exp]
+       );
+
+julia> x1, x2 = GraphNode(feature=1), GraphNode(feature=2)
+(x1, x2)
+
+julia> y = sin(x1) + 1.5
+sin(x1) + 1.5
+
+julia> z = exp(y) + y
+exp(sin(x1) + 1.5) + {(sin(x1) + 1.5)}
+```
+
+Here, the curly braces `{}` indicate that the node
+is shared by another (or more) parent node.
+
+This means that we only need to change it once
+to have changes propagate across the expression:
+
+```julia
+julia> y.r.val *= 0.9
+1.35
+
+julia> z
+exp(sin(x1) + 1.35) + {(sin(x1) + 1.35)}
+```
+
+This also means there are fewer nodes to describe an expression:
+
+```julia
+julia> length(z)
+6
+
+julia> length(convert(Node, z))
+10
+```
+
+where we have converted the `GraphNode` to a `Node` type,
+which breaks shared connections into separate nodes.
+
+## Abstract Types
+
+Both the `Node` and `GraphNode` types are subtypes of the abstract type:
+
+```@docs
+AbstractExpressionNode{T}
 ```
 
-There is also an abstract type `AbstractNode` which is a supertype of `Node`:
+which can be used to create additional expression-like types.
+The supertype of this abstract type is the `AbstractNode` type,
+which is more generic but does not have all of the same methods:
 
 ```@docs
-AbstractNode
+AbstractNode{T}
 ```

ext/DynamicExpressionsSymbolicUtilsExt.jl

@@ -1,7 +1,8 @@
 module DynamicExpressionsSymbolicUtilsExt
 
 using SymbolicUtils
-import DynamicExpressions.EquationModule: Node, DEFAULT_NODE_TYPE
+import DynamicExpressions.EquationModule:
+    AbstractExpressionNode, Node, constructorof, DEFAULT_NODE_TYPE
 import DynamicExpressions.OperatorEnumModule: AbstractOperatorEnum
 import DynamicExpressions.UtilsModule: isgood, isbad, @return_on_false, deprecate_varmap
 import DynamicExpressions.ExtensionInterfaceModule: node_to_symbolic, symbolic_to_node
@@ -19,14 +20,17 @@ end
 subs_bad(x) = isgood(x) ? x : Inf
 
 function parse_tree_to_eqs(
-    tree::Node{T}, operators::AbstractOperatorEnum, index_functions::Bool=false
+    tree::AbstractExpressionNode{T},
+    operators::AbstractOperatorEnum,
+    index_functions::Bool=false,
 ) where {T}
     if tree.degree == 0
         # Return constant if needed
         tree.constant && return subs_bad(tree.val::T)
         return SymbolicUtils.Sym{LiteralReal}(Symbol("x$(tree.feature)"))
     end
     # Collect the next children
+    # TODO: Type instability!
     children = tree.degree == 2 ? (tree.l, tree.r) : (tree.l,)
     # Get the operation
     op = tree.degree == 2 ? operators.binops[tree.op] : operators.unaops[tree.op]
@@ -66,11 +70,12 @@ convert_to_function(x, operators::AbstractOperatorEnum) = x
 function split_eq(
     op,
     args,
-    operators::AbstractOperatorEnum;
+    operators::AbstractOperatorEnum,
+    ::Type{N}=Node;
     variable_names::Union{Array{String,1},Nothing}=nothing,
     # Deprecated:
     varMap=nothing,
-)
+) where {N<:AbstractExpressionNode}
     variable_names = deprecate_varmap(variable_names, varMap, :split_eq)
     !(op ∈ (sum, prod, +, *)) && throw(error("Unsupported operation $op in expression!"))
     if Symbol(op) == Symbol(sum)
@@ -80,10 +85,10 @@ function split_eq(
     else
         ind = findoperation(op, operators.binops)
     end
-    return Node(
+    return constructorof(N)(
         ind,
-        convert(Node, args[1], operators; variable_names=variable_names),
-        convert(Node, op(args[2:end]...), operators; variable_names=variable_names),
+        convert(N, args[1], operators; variable_names=variable_names),
+        convert(N, op(args[2:end]...), operators; variable_names=variable_names),
     )
 end
 
@@ -96,7 +101,7 @@ end
 
 function Base.convert(
     ::typeof(SymbolicUtils.Symbolic),
-    tree::Node,
+    tree::AbstractExpressionNode,
     operators::AbstractOperatorEnum;
     variable_names::Union{Array{String,1},Nothing}=nothing,
     index_functions::Bool=false,
@@ -109,20 +114,22 @@ function Base.convert(
     )
 end
 
-function Base.convert(::typeof(Node), x::Number, operators::AbstractOperatorEnum; kws...)
-    return Node(; val=DEFAULT_NODE_TYPE(x))
+function Base.convert(
+    ::Type{N}, x::Number, operators::AbstractOperatorEnum; kws...
+) where {N<:AbstractExpressionNode}
+    return constructorof(N)(; val=DEFAULT_NODE_TYPE(x))
 end
 
 function Base.convert(
-    ::typeof(Node),
+    ::Type{N},
     expr::SymbolicUtils.Symbolic,
     operators::AbstractOperatorEnum;
     variable_names::Union{Array{String,1},Nothing}=nothing,
-)
+) where {N<:AbstractExpressionNode}
     variable_names = deprecate_varmap(variable_names, nothing, :convert)
     if !SymbolicUtils.istree(expr)
-        variable_names === nothing && return Node(String(expr.name))
-        return Node(String(expr.name), variable_names)
+        variable_names === nothing && return constructorof(N)(String(expr.name))
+        return constructorof(N)(String(expr.name), variable_names)
     end
 
     # First, we remove integer powers:
@@ -134,20 +141,21 @@ function Base.convert(
     op = convert_to_function(SymbolicUtils.operation(expr), operators)
     args = SymbolicUtils.arguments(expr)
 
-    length(args) > 2 && return split_eq(op, args, operators; variable_names=variable_names)
+    length(args) > 2 &&
+        return split_eq(op, args, operators, N; variable_names=variable_names)
     ind = if length(args) == 2
         findoperation(op, operators.binops)
     else
         findoperation(op, operators.unaops)
     end
 
-    return Node(
-        ind, map(x -> convert(Node, x, operators; variable_names=variable_names), args)...
+    return constructorof(N)(
+        ind, map(x -> convert(N, x, operators; variable_names=variable_names), args)...
     )
 end
 
 """
-    node_to_symbolic(tree::Node, operators::AbstractOperatorEnum;
+    node_to_symbolic(tree::AbstractExpressionNode, operators::AbstractOperatorEnum;
                 variable_names::Union{Array{String, 1}, Nothing}=nothing,
                 index_functions::Bool=false)
 
@@ -156,17 +164,17 @@ will generate a symbolic equation in SymbolicUtils.jl format.
 
 ## Arguments
 
-- `tree::Node`: The equation to convert.
+- `tree::AbstractExpressionNode`: The equation to convert.
 - `operators::AbstractOperatorEnum`: OperatorEnum, which contains the operators used in the equation.
 - `variable_names::Union{Array{String, 1}, Nothing}=nothing`: What variable names to use for
     each feature. Default is [x1, x2, x3, ...].
 - `index_functions::Bool=false`: Whether to generate special names for the
-    operators, which then allows one to convert back to a `Node` format
+    operators, which then allows one to convert back to a `AbstractExpressionNode` format
     using `symbolic_to_node`.
     (CURRENTLY UNAVAILABLE - See https://github.com/MilesCranmer/SymbolicRegression.jl/pull/84).
 """
 function node_to_symbolic(
-    tree::Node,
+    tree::AbstractExpressionNode,
     operators::AbstractOperatorEnum;
     variable_names::Union{Array{String,1},Nothing}=nothing,
     index_functions::Bool=false,
@@ -192,13 +200,14 @@ end
 
 function symbolic_to_node(
     eqn::SymbolicUtils.Symbolic,
-    operators::AbstractOperatorEnum;
+    operators::AbstractOperatorEnum,
+    ::Type{N}=Node;
     variable_names::Union{Array{String,1},Nothing}=nothing,
     # Deprecated:
     varMap=nothing,
-)::Node
+) where {N<:AbstractExpressionNode}
     variable_names = deprecate_varmap(variable_names, varMap, :symbolic_to_node)
-    return convert(Node, eqn, operators; variable_names=variable_names)
+    return convert(N, eqn, operators; variable_names=variable_names)
 end
 
 function multiply_powers(eqn::Number)::Tuple{SYMBOLIC_UTILS_TYPES,Bool}

src/DynamicExpressions.jl

@@ -15,13 +15,16 @@ import PackageExtensionCompat: @require_extensions
 import Reexport: @reexport
 @reexport import .EquationModule:
     AbstractNode,
+    AbstractExpressionNode,
+    GraphNode,
     Node,
     string_tree,
     print_tree,
     copy_node,
     set_node!,
     tree_mapreduce,
     filter_map
+import .EquationModule: constructorof, preserve_sharing
 @reexport import .EquationUtilsModule:
     count_nodes,
     count_constants,
@@ -38,7 +41,7 @@ import Reexport: @reexport
 @reexport import .EvaluateEquationModule: eval_tree_array, differentiable_eval_tree_array
 @reexport import .EvaluateEquationDerivativeModule:
     eval_diff_tree_array, eval_grad_tree_array
-@reexport import .SimplifyEquationModule: combine_operators, simplify_tree
+@reexport import .SimplifyEquationModule: combine_operators, simplify_tree!
 @reexport import .EvaluationHelpersModule
 @reexport import .ExtensionInterfaceModule: node_to_symbolic, symbolic_to_node