Machines

Under the hood, calling fit! on a machine calls either MLJBase.fit or MLJBase.update, depending on the machine's internal state (as recorded in private fields old_model and old_rows). These lower-level fit and update methods, which are not ordinarily called directly by the user, dispatch on the model and a view of the data defined by the optional rows keyword argument of fit! (all rows by default). In this way, if a model update method has been implemented for the model, calls to fit! can avoid redundant calculations for certain kinds of model mutations (eg, increasing the number of epochs in a neural network).

using MLJ; color_off() # hide
forest = EnsembleModel(atom=(@load DecisionTreeClassifier), n=10);
X, y = @load_iris;
mach = machine(forest, X, y)
fit!(mach, verbosity=2);

Generally, changing a hyperparameter triggers retraining on calls to subsequent fit!:

julia> forest.bagging_fraction=0.5
ERROR: UndefVarError: forest not defined

julia> fit!(mach, verbosity=2);
ERROR: UndefVarError: mach not defined

However, for this iterative model, increasing the iteration parameter only adds models to the existing ensemble:

julia> forest.n=15
ERROR: UndefVarError: forest not defined

julia> fit!(mach, verbosity=2);
ERROR: UndefVarError: mach not defined

Call fit! again without making a change and no retraining occurs:

julia> fit!(mach);
ERROR: UndefVarError: mach not defined

However, retraining can be forced:

julia> fit!(mach, force=true);
ERROR: UndefVarError: mach not defined

And is re-triggered if the view of the data changes:

julia> fit!(mach, rows=1:100);
ERROR: UndefVarError: mach not defined
julia> fit!(mach, rows=1:100);
ERROR: UndefVarError: mach not defined

Inspecting machines

There are two methods for inspecting the outcomes of training in MLJ. To obtain a named-tuple describing the learned parameters (in a user-friendly way where possible) use fitted_params(mach). All other training-related outcomes are inspected with report(mach).

X, y = @load_iris
pca = @load PCA
mach = machine(pca, X)
fit!(mach)
Machine{PCA} @969 trained 1 time.
  args: 
    1:	Source @537 ⏎ `Table{AbstractArray{Continuous,1}}`
julia> fitted_params(mach)
(projection = [-0.3615896773814497 0.656539883285832 0.5809972798276167; 0.08226888989221419 0.7297123713264958 -0.596418087938103; -0.8565721052905279 -0.17576740342865457 -0.07252407548696274; -0.3588439262482157 -0.07470647013503341 -0.549060910726604],)

julia> report(mach)
(indim = 4,
 outdim = 3,
 tprincipalvar = 4.545608248041779,
 tresidualvar = 0.02368302712600201,
 tvar = 4.569291275167781,
 mean = [5.8433333333333355, 3.054000000000001, 3.7586666666666697, 1.1986666666666674],
 principalvars = [4.224840768320109, 0.24224357162751542, 0.07852390809415459],)
MLJModelInterface.fitted_paramsFunction
fitted_params(mach)

Return the learned parameters for a machine mach that has been fit!, for example the coefficients in a linear model.

This is a named tuple and human-readable if possible.

If mach is a machine for a composite model, such as a model constructed using @pipeline, then the returned named tuple has the composite type's field names as keys. The corresponding value is the fitted parameters for the machine in the underlying learning network bound to that model. (If multiple machines share the same model, then the value is a vector.)

using MLJ
@load LogisticClassifier pkg=MLJLinearModels
X, y = @load_crabs;
pipe = @pipeline Standardizer LogisticClassifier
mach = machine(pipe, X, y) |> fit!

julia> fitted_params(mach).logistic_classifier
(classes = CategoricalArrays.CategoricalValue{String,UInt32}["B", "O"],
 coefs = Pair{Symbol,Float64}[:FL => 3.7095037897680405, :RW => 0.1135739140854546, :CL => -1.6036892745322038, :CW => -4.415667573486482, :BD => 3.238476051092471],
 intercept = 0.0883301599726305,)

Additional keys, machines and fitted_params_given_machine, give a list of all machines in the underlying network, and a dictionary of fitted parameters keyed on those machines.

```

MLJBase.reportFunction
report(mach)

Return the report for a machine mach that has been fit!, for example the coefficients in a linear model.

This is a named tuple and human-readable if possible.

If mach is a machine for a composite model, such as a model constructed using @pipeline, then the returned named tuple has the composite type's field names as keys. The corresponding value is the report for the machine in the underlying learning network bound to that model. (If multiple machines share the same model, then the value is a vector.)

using MLJ
@load LinearBinaryClassifier pkg=GLM
X, y = @load_crabs;
pipe = @pipeline Standardizer LinearBinaryClassifier
mach = machine(pipe, X, y) |> fit!

julia> report(mach).linear_binary_classifier
(deviance = 3.8893386087844543e-7,
 dof_residual = 195.0,
 stderror = [18954.83496713119, 6502.845740757159, 48484.240246060406, 34971.131004997274, 20654.82322484894, 2111.1294584763386],
 vcov = [3.592857686311793e8 9.122732393971942e6 … -8.454645589364915e7 5.38856837634321e6; 9.122732393971942e6 4.228700272808351e7 … -4.978433790526467e7 -8.442545425533723e6; … ; -8.454645589364915e7 -4.978433790526467e7 … 4.2662172244975924e8 2.1799125705781363e7; 5.38856837634321e6 -8.442545425533723e6 … 2.1799125705781363e7 4.456867590446599e6],)

Additional keys, machines and report_given_machine, give a list of all machines in the underlying network, and a dictionary of reports keyed on those machines.

```

Constructing machines

A machine is constructed with the syntax machine(model, args...) where the possibilities for args (called training arguments) are summarized in table below. Here X and y represent inputs and target, respectively, and Xout the output of a transform call. Machines for supervised models may have additional training arguments, such as a vector of per-observation weights (in which case supports_weights(model) == true).

model supertypemachine constructor callsoperation calls (first compulsory)
Deterministic <: Supervisedmachine(model, X, y, extras...)predict(mach, Xnew), transform(mach, Xnew), inverse_transform(mach, Xout)
Probabilistic <: Supervisedmachine(model, X, y, extras...)predict(mach, Xnew), predict_mean(mach, Xnew), predict_median(mach, Xnew), predict_mode(mach, Xnew), transform(mach, Xnew), inverse_transform(mach, Xout)
Unsupervised (except Static)machine(model, X)transform(mach, Xnew), inverse_transform(mach, Xout), predict(mach, Xnew)
Staticmachine(model)transform(mach, Xnews...), inverse_transform(mach, Xout)

All operations on machines (predict, transform, etc) have exactly one argument (Xnew or Xout above) after mach, the machine instance. An exception is a machine bound to a Static model, which can have any number of arguments after mach. For more on Static transformers (which have no training arguments) see Static transformers.

A machine is reconstructed from a file using the syntax machine("my_machine.jlso"), or machine("my_machine.jlso", args...) if retraining using new data. See Saving machines below.

Constructing machines in learning networks

Instead of data X, y, etc, the machine constructor is provided Node or Source objects ("dynamic data") when building a learning network. See Composing Models for more on this advanced feature. One also uses machine to wrap a machine around a whole learning network; see Learning network machines.

Saving machines

To save a machine to file, use the MLJ.save command:

tree = @load DecisionTreeClassifier
mach = fit!(machine(tree, X, y))
MLJ.save("my_machine.jlso", mach)

To de-serialize, one uses the machine constructor:

mach2 = machine("my_machine.jlso")
predict(mach2, Xnew);

The machine mach2 cannot be retrained; however, by providing data to the constructor one can enable retraining using the saved model hyperparameters (which overwrites the saved learned parameters):

mach3 = machine("my_machine.jlso", Xnew, ynew)
fit!(mach3)

Internals

For a supervised machine the predict method calls a lower-level MLJBase.predict method, dispatched on the underlying model and the fitresult (see below). To see predict in action, as well as its unsupervised cousins transform and inverse_transform, see Getting Started.

The fields of a Machine instance (which should not generally be accessed by the user) are:

  • model - the struct containing the hyperparameters to be used in calls to fit!

  • fitresult - the learned parameters in a raw form, initially undefined

  • args - a tuple of the data, each element wrapped in a source node; see Learning Networks (in the supervised learning example above, args = (source(X), source(y)))

  • report - outputs of training not encoded in fitresult (eg, feature rankings)

  • old_model - a deep copy of the model used in the last call to fit!

  • old_rows - a copy of the row indices used in last call to fit!

  • cache

The interested reader can learn more on machine internals by examining the simplified code excerpt in Internals.

API Reference

MLJBase.machineFunction
machine(model, args...)

Construct a Machine object binding a model, storing hyper-parameters of some machine learning algorithm, to some data, args. When building a learning network, Node objects can be substituted for concrete data.

machine(Xs; oper1=node1, oper2=node2)
machine(Xs, ys; oper1=node1, oper2=node2)
machine(Xs, ys, extras...; oper1=node1, oper2=node2, ...)

Construct a special machine called a learning network machine, that "wraps" a learning network, usually in preparation to export the network as a stand-alone composite model type. The keyword arguments declare what nodes are called when operations, such as predict and transform, are called on the machine.

In addition to the operations named in the constructor, the methods fit!, report, and fitted_params can be applied as usual to the machine constructed.

machine(Probablistic(), args...; kwargs...)
machine(Deterministic(), args...; kwargs...)
machine(Unsupervised(), args...; kwargs...)
machine(Static(), args...; kwargs...)

Same as above, but specifying explicitly the kind of model the learning network is to meant to represent.

Learning network machines are not to be confused with an ordinary machine that happens to be bound to a stand-alone composite model (i.e., an exported learning network).

Examples

Supposing a supervised learning network's final predictions are obtained by calling a node yhat, then the code

mach = machine(Deterministic(), Xs, ys; predict=yhat)
fit!(mach; rows=train)
predictions = predict(mach, Xnew) # `Xnew` concrete data

is equivalent to

fit!(yhat, rows=train)
predictions = yhat(Xnew)

Here Xs and ys are the source nodes receiving, respectively, the input and target data.

In a unsupervised learning network for clustering, with single source node Xs for inputs, and in which the node Xout delivers the output of dimension reduction, and yhat the class labels, one can write

mach = machine(Unsupervised(), Xs; transform=Xout, predict=yhat)
fit!(mach)
transformed = transform(mach, Xnew) # `Xnew` concrete data
predictions = predict(mach, Xnew)

which is equivalent to

fit!(Xout)
fit!(yhat)
transformed = Xout(Xnew)
predictions = yhat(Xnew)
StatsBase.fit!Function
fit!(mach::Machine, rows=nothing, verbosity=1, force=false)

Fit the machine mach. In the case that mach has Node arguments, first train all other machines on which mach depends.

To attempt to fit a machine without touching any other machine, use fit_only!. For more on the internal logic of fitting see fit_only!

fit!(N::Node;
     rows=nothing,
     verbosity=1,
     force=false,
     acceleration=CPU1())

Train all machines required to call the node N, in an appropriate order. These machines are those returned by machines(N).

fit!(mach::Machine{<:Surrogate};
     rows=nothing,
     acceleration=CPU1(),
     verbosity=1,
     force=false))

Train the complete learning network wrapped by the machine mach.

More precisely, if s is the learning network signature used to construct mach, then call fit!(N), where N = glb(values(s)...) is a greatest lower bound on the nodes appearing in the signature. For example, if s = (predict=yhat, transform=W), then call fit!(glb(yhat, W)). Here glb is tuple overloaded for nodes.

See also machine

MLJBase.fit_only!Function
MLJBase.fit_only!(mach::Machine; rows=nothing, verbosity=1, force=false)

Without mutating any other machine on which it may depend, perform one of the following actions to the machine mach, using the data and model bound to it, and restricting the data to rows if specified:

  • Ab initio training. Ignoring any previous learned parameters and cache, compute and store new learned parameters. Increment mach.state.

  • Training update. Making use of previous learned parameters and/or cache, replace or mutate existing learned parameters. The effect is the same (or nearly the same) as in ab initio training, but may be faster or use less memory, assuming the model supports an update option (implements MLJBase.update). Increment mach.state.

  • No-operation. Leave existing learned parameters untouched. Do not increment mach.state.

Training action logic

For the action to be a no-operation, either mach.frozen == true or none of the following apply:

  • (i) mach has never been trained (mach.state == 0).

  • (ii) force == true

  • (iii) The state of some other machine on which mach depends has changed since the last time mach was trained (ie, the last time mach.state was last incremented)

  • (iv) The specified rows have changed since the last retraining.

  • (v) mach.model has changed since the last retraining.

In cases (i) - (iv), mach is trained ab initio. In case (v) a training update is applied.

To freeze or unfreeze mach, use freeze!(mach) or thaw!(mach).

Implementation detail

The data to which a machine is bound is stored in mach.args. Each element of args is either a Node object, or, in the case that concrete data was bound to the machine, it is concrete data wrapped in a Source node. In all cases, to obtain concrete data for actual training, each argument N is called, as in N() or N(rows=rows), and either MLJBase.fit (ab initio training) or MLJBase.update (training update) is dispatched on mach.model and this data. See the "Adding models for general use" section of the MLJ documentation for more on these lower-level training methods.

MLJModelInterface.saveFunction
MLJ.save(filename, mach::Machine; kwargs...)
MLJ.save(io, mach::Machine; kwargs...)

MLJBase.save(filename, mach::Machine; kwargs...)
MLJBase.save(io, mach::Machine; kwargs...)

Serialize the machine mach to a file with path filename, or to an input/output stream io (at least IOBuffer instances are supported).

The format is JLSO (a wrapper for julia native or BSON serialization). For some model types, a custom serialization will be additionally performed.

Keyword arguments

These keyword arguments are passed to the JLSO serializer:

keywordvaluesdefault
format:julia_serialize, :BSON:julia_serialize
compression:gzip, :none:none

See https://github.com/invenia/JLSO.jl for details.

Any additional keyword arguments are passed to model-specific serializers.

Machines are de-serialized using the machine constructor as shown in the example below. Data (or nodes) may be optionally passed to the constructor for retraining on new data using the saved model.

Example

using MLJ
tree = @load DecisionTreeClassifier
X, y = @load_iris
mach = fit!(machine(tree, X, y))

MLJ.save("tree.jlso", mach, compression=:none)
mach_predict_only = machine("tree.jlso")
predict(mach_predict_only, X)

mach2 = machine("tree.jlso", selectrows(X, 1:100), y[1:100])
predict(mach2, X) # same as above

fit!(mach2) # saved learned parameters are over-written
predict(mach2, X) # not same as above

# using a buffer:
io = IOBuffer()
MLJ.save(io, mach)
seekstart(io)
predict_only_mach = machine(io)
predict(predict_only_mach, X)
Only load files from trusted sources

Maliciously constructed JLSO files, like pickles, and most other general purpose serialization formats, can allow for arbitrary code execution during loading. This means it is possible for someone to use a JLSO file that looks like a serialized MLJ machine as a Trojan horse.