CloudForest implements fast, flexible ensembles of decision trees for machine learning in pure Go (golang to search engines). It allows for a number of related algorithms for classification, regression, feature selection and structure analysis on heterogeneous numerical / categorical data with missing values. These include:
- Breiman and Cutler's Random Forest for Classification and Regression
- Adaptive Boosting (AdaBoost) Classification and Regression
- Gradient Boosting Tree Regression
- Entropy and Cost driven classification
- L1 regression
- Feature selection with artificial contrasts
- Proximity and model structure analysis
- Methods for Classification on Unbalanced Data
CloudForest has been optimized to minimize memory use, allow multi-core and learning with minimal allocations and perform especially well learning from categorical features with a small number of class labels. This includes binary data and genomic variant data which may have class labels like "reference", "heterozygous", "homozygous".
File formats have been chosen to allow multi machine parallel learning.
Command line utilities to grow, apply and analyze forests are provided in sub directories or CloudForest can be used as a library.
This Document covers command line usage, file formats and some algorithmic background.
Documentation for coding against CloudForest has been generated with godoc and can be viewed live at: http://godoc.org/github.com/ryanbressler/CloudForest
Pull requests and bug reports are welcome; Code Repo and Issue tracker can be found at: https://github.com/ryanbressler/CloudForest
CloudForest is being developed in the Shumelivich Lab at the Institute for Systems Biology.
With go and go path set up:
go get github.com/ryanbressler/CloudForest
go install github.com/ryanbressler/CloudForest/growforest
go install github.com/ryanbressler/CloudForest/applyforest
go install github.com/ryanbressler/CloudForest/leafcount#grow a predictor forest with default parameters and save it to forest.sf
growforest -train train.fm -rfpred forest.sf -target B:FeatureName
#grow a 1000 tree forest using, 16 cores and report out of bag error with minimum leafSize 8
growforest -train train.fm -rfpred forest.sf -target B:FeatureName -oob -nThreads 16 -nTrees 1000 -leafSize 8
#grow a 1000 tree forest evaluating half the features as candidates at each split and reporting
#out of bag error after each tree to watch for convergence
growforest -train train.fm -rfpred forest.sf -target B:FeatureName -mTry .5 -progress
#growforest with weighted random forest
growforest -train train.fm -rfpred forest.sf -target B:FeatureName -rfweights '{"true":2,"false":0.5}'
#report all growforest options
growforest -h
#Print the (balanced for classification, least squares for regression error rate on test data to standard out
applyforest -fm test.fm -rfpred forest.sf
#Apply the forest, report errorrate and save predictions
#Predictions are output in a tsv as:
#CaseLabel Predicted Actual
applyforest -fm test.fm -rfpred forest.sf -preds predictions.tsv
#Calculate counts of case vs case (leaves) and case vs feature (branches) proximity.
#Leaves are reported as:
#Case1 Case2 Count
#Branches Are Reported as:
#Case Feature Count
leafcount -train train.fm -rfpred forest.sf -leaves leaves.tsv -branches branches.tsvgrowforest trains a forest using the following parameters which can be listed with -h
Parameter's are implemented using go's parameter parser so that boolean parameters can be set to true with a simple flag:
#the following are equivalent
growforest -oob
growforest -oob=true
And equals signs and quotes are optional for other parameters:
#the following are equivalent
growforest -train featurematrix.afm
growforest -train="featurematrix.afm"
Basic options
-target="": The row header of the target in the feature matrix.
-train="featurematrix.afm": AFM formated feature matrix containing training data.
-rfpred="rface.sf": File name to output predictor forest in sf format.
-leafSize="0": The minimum number of cases on a leaf node. If <=0 will be inferred to 1 for classification 4 for regression.
-mTry="0": Number of candidate features for each split as a count (ex: 10) or portion of total (ex: .5). Ceil(sqrt(nFeatures)) if <=0.
-nSamples="0": The number of cases to sample (with replacement) for each tree as a count (ex: 10) or portion of total (ex: .5). If <=0 set to total number of cases.
-nTrees=100: Number of trees to grow in the predictor.
-importance="": File name to output importance.
-oob=false: Calculate and report oob error.
Advanced Options
-blacklist="": A list of feature id's to exclude from the set of predictors.
-includeRE="": Filter features that DON'T match this RE.
-blockRE="": A regular expression to identify features that should be filtered out.
-impute=false: Impute missing values to feature mean/mode before growth.
-nCores=1: The number of cores to use.
-progress=false: Report tree number and running oob error.
-oobpreds="": Calculate and report oob predictions in the file specified.
-cpuprofile="": write cpu profile to file
-multiboost=false: Allow multithreaded boosting which msy have unexpected results. (highly experimental)
-nobag=false: Don't bag samples for each tree.
-splitmissing=false: Split missing values onto a third branch at each node (experimental).
Regression Options
-gbt=0: Use gradient boosting with the specified learning rate.
-l1=false: Use l1 norm regression (target must be numeric).
-ordinal=false: Use ordinal regression (target must be numeric).
-adaboost=false: Use Adaptive boosting (highly experimental for regression).
Classification Options
-adaboost=false: Use Adaptive boosting for classification.
-balance=false: Balance bagging of samples by target class for unbalanced classification.
-cost="": For categorical targets, a json string to float map of the cost of falsely identifying each category.
-entropy=false: Use entropy minimizing classification (target must be categorical).
-rfweights="": For categorical targets, a json string to float map of the weights to use for each category in Weighted RF.
Note: rfweights and cost should use json to specify the weights and or costs per class using the strings used to represent the class in the boolean or categorical feature:
growforest -rfweights '{"true":2,"false":0.5}'
Randomizing Data
Randomizing shuffling parts of the data or including shuffled "Artifichal Contrasts" can be useful to establish baselines for comparison.
-permutate=false: Permutate the target feature (to establish random predictive power).
-contrastall=false: Include a shuffled artificial contrast copy of every feature.
-nContrasts=0: The number of randomized artificial contrast features to include in the feature matrix.
-shuffleRE="": A regular expression to identify features that should be shuffled.
applyforest applies a forest to the specified feature matrix and outputs predictions as a two column (caselabel predictedvalue) tsv.
Usage of applyforest:
-fm="featurematrix.afm": AFM formated feature matrix containing data.
-mean=false: Force numeric (mean) voteing.
-mode=false: Force catagorical (mode) voteing.
-preds="": The name of a file to write the predictions into.
-rfpred="rface.sf": A predictor forest.
leafcount outputs counts of case case co-occurrence on leaf nodes (leaves.tsv, Brieman's proximity) and counts of the number of times a feature is used to split a node containing each case (branches.tsv a measure of relative/local importance).
Usage of leafcount:
-branches="branches.tsv": a case by feature sparse matrix of leaf co-occurrence in tsv format
-fm="featurematrix.afm": AFM formated feature matrix to use.
-leaves="leaves.tsv": a case by case sparse matrix of leaf co-occurrence in tsv format
-rfpred="rface.sf": A predictor forest.
errorrate calculates the error of a forest vs a testing data set and reports it to standard out
Usage of errorrate:
-fm="featurematrix.afm": AFM formated feature matrix containing test data.
-rfpred="rface.sf": A predictor forest.
Variable Importance in CloudForest is based on the as the mean decrease in impurity over all of the splits made using a feature. It is output in a tsv as:
Feature DecreasePerUse UseCount DecresePerTree DecresePerTreeUsed TreeUsedCount MeanMinimalDepth
Where DecresePerTree is calculated over all trees, not just the ones the feature was used in and DecresePerTree.
Each of these scores has different properties:
- Per-use and per-tree-used scores may be more resistant to feature redundancy,
- Per-tree-used and per-tree scores may better pick out complex effects.
- Mean Minimal Depth has been proposed (see "Random Survival Forests") as an alternative importance.
To provide a baseline for evaluating importance, artificial contrast features can be used by including shuffled copies of existing features (-nContrasts, -contrastAll).
A feature that performs well when randomized (or when the target has been randomized) may be causing overfitting.
The option to permutate the target (-permutate) will establish a minimum random baseline. Using a regular expression (-shuffleRE) to shuffle part of the data can be useful in teasing out the contributions of different subsets of features.
CloudForest borrows the annotated feature matrix (.afm) and stochastic forest (.sf) file formats from Timo Erkkila's rf-ace which can be found at https://code.google.com/p/rf-ace/
An annotated feature matrix (.afm) file is a tab delineated file with column and row headers. Columns represent cases and rows represent features. A row header / feature id includes a prefix to specify the feature type
"N:" Prefix for numerical feature id.
"C:" Prefix for categorical feature id.
"B:" Prefix for boolean feature id.
Categorical and boolean features use strings for their category labels. Missing values are represented by "?","nan","na", or "null" (case insensitive). A short example:
featureid case1 case2 case3
N:NumF1 0.0 .1 na
C:CatF2 red red green
A stochastic forest (.sf) file contains a forest of decision trees. The main advantage of this format as opposed to an established format like json is that an sf file can be written iteratively tree by tree and multiple .sf files can be combined with minimal logic required allowing for massively parallel growth of forests with low memory use.
An .sf file consists of lines each of which is a comma separated list of key value pairs. Lines can designate either a FOREST, TREE, or NODE. Each tree belongs to the preceding forest and each node to the preceding tree. Nodes must be written in order of increasing depth.
CloudForest generates fewer fields then rf-ace but requires the following. Other fields will be ignored
Forest requires forest type (only RF currently), target and ntrees:
FOREST=RF|GBT|..,TARGET="$feature_id",NTREES=int
Tree requires only an int and the value is ignored though the line is needed to designate a new tree:
TREE=int
Node requires a path encoded so that the root node is specified by "*" and each split left or right as "L" or "R". Leaf nodes should also define PRED such as "PRED=1.5" or "PRED=red". Splitter nodes should define SPLITTER with a feature id inside of double quotes, SPLITTERTYPE=[CATEGORICAL|NUMERICAL] and a LVALUE term which can be either a float inside of double quotes representing the highest value sent left or a ":" separated list of categorical values sent left.
NODE=$path,PRED=[float|string],SPLITTER="$feature_id",SPLITTERTYPE=[CATEGORICAL|NUMERICAL] LVALUES="[float|: separated list"
An example .sf file:
FOREST=RF,TARGET="N:CLIN:TermCategory:NB::::",NTREES=12800
TREE=0
NODE=*,PRED=3.48283,SPLITTER="B:SURV:Family_Thyroid:F::::maternal",SPLITTERTYPE=CATEGORICAL,LVALUES="false"
NODE=*L,PRED=3.75
NODE=*R,PRED=1
Cloud forest can parse and apply .sf files generated by at least some versions of rf-ace.
When compiled with go1.1 CloudForest achieves running times similar to implementations in other languages. Using gccgo (4.8.0 at least) results in longer running times and is not recommended. This may change as gcc go addopts the go 1.1 way of implementing closures.
The idea for (and trademark of the term) Random Forests originated with Leo Brieman and Adele Cuttler. Their code and paper's can be found at:
http://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm
All code in CloudForest is original but some ideas for methods and optimizations were inspired by Timo Erkilla's rf-ace and Andy Liaw and Matthew Wiener randomForest R package based on Brieman and Cuttler's code:
https://code.google.com/p/rf-ace/ http://cran.r-project.org/web/packages/randomForest/index.html
The idea for Artificial Contrasts was found in: Eugene Tuv, Alexander Borisov, George Runger and Kari Torkkola's paper "Feature Selection with Ensembles, Artificial Variables, and Redundancy Elimination" http://www.researchgate.net/publication/220320233_Feature_Selection_with_Ensembles_Artificial_Variables_and_Redundancy_Elimination/file/d912f5058a153a8b35.pdf
The idea for growing trees to minimize categorical entropy comes from Ross Quinlan's ID3: http://en.wikipedia.org/wiki/ID3_algorithm
"The Elements of Statistical Learning" 2nd edition by Trevor Hastie, Robert Tibshirani and Jerome Friedman was also consulted during development.
Methods for classification from unbalanced data are covered in several papers: http://statistics.berkeley.edu/sites/default/files/tech-reports/666.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163175/ http://www.biomedcentral.com/1471-2105/11/523 http://bib.oxfordjournals.org/content/early/2012/03/08/bib.bbs006 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067863