예제 #1
0
func main() {
	fm := flag.String("fm",
		"featurematrix.afm", "AFM formated feature matrix containing data.")
	rf := flag.String("rfpred",
		"rface.sf", "A predictor forest.")
	predfn := flag.String("preds",
		"", "The name of a file to write the predictions into.")
	votefn := flag.String("votes",
		"", "The name of a file to write categorical vote totals to.")
	var num bool
	flag.BoolVar(&num, "mean", false, "Force numeric (mean) voting.")
	var sum bool
	flag.BoolVar(&sum, "sum", false, "Force numeric sum voting (for gradient boosting etc).")
	var expit bool
	flag.BoolVar(&expit, "expit", false, "Expit (inverst logit) transform data (for gradient boosting classification).")
	var cat bool
	flag.BoolVar(&cat, "mode", false, "Force categorical (mode) voting.")

	flag.Parse()

	//Parse Data
	data, err := CloudForest.LoadAFM(*fm)
	if err != nil {
		log.Fatal(err)
	}

	forestfile, err := os.Open(*rf) // For read access.
	if err != nil {
		log.Fatal(err)
	}
	defer forestfile.Close()
	forestreader := CloudForest.NewForestReader(forestfile)
	forest, err := forestreader.ReadForest()
	if err != nil {
		log.Fatal(err)
	}

	var predfile *os.File
	if *predfn != "" {
		predfile, err = os.Create(*predfn)
		if err != nil {
			log.Fatal(err)
		}
		defer predfile.Close()
	}

	var bb CloudForest.VoteTallyer
	switch {
	case sum:
		bb = CloudForest.NewSumBallotBox(data.Data[0].Length())

	case !cat && (num || strings.HasPrefix(forest.Target, "N")):
		bb = CloudForest.NewNumBallotBox(data.Data[0].Length())

	default:
		bb = CloudForest.NewCatBallotBox(data.Data[0].Length())
	}

	for _, tree := range forest.Trees {
		tree.Vote(data, bb)
	}

	targeti, hasTarget := data.Map[forest.Target]
	if hasTarget {
		fmt.Printf("Target is %v in feature %v\n", forest.Target, targeti)
		er := bb.TallyError(data.Data[targeti])
		fmt.Printf("Error: %v\n", er)
	}
	if *predfn != "" {
		fmt.Printf("Outputting label predicted actual tsv to %v\n", *predfn)
		for i, l := range data.CaseLabels {
			actual := "NA"
			if hasTarget {
				actual = data.Data[targeti].GetStr(i)
			}

			result := ""

			if sum || forest.Intercept != 0.0 {
				numresult := 0.0
				if sum {
					numresult = bb.(*CloudForest.SumBallotBox).TallyNum(i) + forest.Intercept
				} else {
					numresult = bb.(*CloudForest.NumBallotBox).TallyNum(i) + forest.Intercept
				}
				if expit {
					numresult = CloudForest.Expit(numresult)
				}
				result = fmt.Sprintf("%v", numresult)

			} else {
				result = bb.Tally(i)
			}
			fmt.Fprintf(predfile, "%v\t%v\t%v\n", l, result, actual)
		}
	}

	//Not thread safe code!
	if *votefn != "" {
		fmt.Printf("Outputting vote totals to %v\n", *votefn)
		cbb := bb.(*CloudForest.CatBallotBox)
		votefile, err := os.Create(*votefn)
		if err != nil {
			log.Fatal(err)
		}
		defer votefile.Close()
		fmt.Fprintf(votefile, ".")

		for _, lable := range cbb.CatMap.Back {
			fmt.Fprintf(votefile, "\t%v", lable)
		}
		fmt.Fprintf(votefile, "\n")

		for i, box := range cbb.Box {
			fmt.Fprintf(votefile, "%v", data.CaseLabels[i])

			for j := range cbb.CatMap.Back {
				total := 0.0
				total = box.Map[j]

				fmt.Fprintf(votefile, "\t%v", total)

			}
			fmt.Fprintf(votefile, "\n")

		}
	}
}
예제 #2
0
파일: main.go 프로젝트: lytics/CloudForest
func main() {
	fm := flag.String("data",
		"", "Data file to read.")

	outfn := flag.String("out",
		"", "The name of a file to write feature matrix too.")

	libsvmtarget := flag.String("libsvmtarget",
		"", "Output lib svm with the named feature in the first position.")

	anontarget := flag.String("anontarget",
		"", "Strip strings with named feature in the first position.")

	blacklist := flag.String("blacklist",
		"", "A list of feature id's to exclude from the set of predictors.")

	flag.Parse()

	//Parse Data
	data, err := CloudForest.LoadAFM(*fm)
	if err != nil {
		log.Fatal(err)
	}

	blacklisted := 0
	blacklistis := make([]bool, len(data.Data))
	if *blacklist != "" {
		fmt.Printf("Loading blacklist from: %v\n", *blacklist)
		blackfile, err := os.Open(*blacklist)
		if err != nil {
			log.Fatal(err)
		}
		tsv := csv.NewReader(blackfile)
		tsv.Comma = '\t'
		for {
			id, err := tsv.Read()
			if err == io.EOF {
				break
			} else if err != nil {
				log.Fatal(err)
			}
			if id[0] == *anontarget || id[0] == *libsvmtarget {
				continue
			}
			i, ok := data.Map[id[0]]
			if !ok {
				fmt.Printf("Ignoring blacklist feature not found in data: %v\n", id[0])
				continue
			}
			if !blacklistis[i] {
				blacklisted += 1
				blacklistis[i] = true
			}

		}
		blackfile.Close()

	}

	newdata := make([]CloudForest.Feature, 0, len(data.Data)-blacklisted)
	newmap := make(map[string]int, len(data.Data)-blacklisted)

	for i, f := range data.Data {
		if !blacklistis[i] {
			newmap[f.GetName()] = len(newdata)
			newdata = append(newdata, f)
		}
	}

	data.Data = newdata
	data.Map = newmap

	if *anontarget != "" {
		data.StripStrings(*anontarget)

	}

	//anotate with type information
	for _, f := range data.Data {
		switch f.(type) {
		case *CloudForest.DenseNumFeature:
			nf := f.(*CloudForest.DenseNumFeature)
			if !strings.HasPrefix(nf.Name, "N:") {
				nf.Name = "N:" + nf.Name
			}
		case *CloudForest.DenseCatFeature:
			nf := f.(*CloudForest.DenseCatFeature)
			if !(strings.HasPrefix(nf.Name, "C:") || strings.HasPrefix(nf.Name, "B:")) {
				nf.Name = "C:" + nf.Name
			}

		}
	}

	ncases := data.Data[0].Length()
	cases := make([]int, ncases, ncases)

	for i := 0; i < ncases; i++ {
		cases[i] = i
	}

	outfile, err := os.Create(*outfn)
	if err != nil {
		log.Fatal(err)
	}
	defer outfile.Close()

	if *libsvmtarget == "" {

		err = data.WriteCases(outfile, cases)
		if err != nil {
			log.Fatal(err)
		}
	} else {
		// targeti, ok := data.Map[*libsvmtarget]
		// if !ok {
		// 	log.Fatalf("Target '%v' not found in data.", *libsvmtarget)
		// }
		// target := data.Data[targeti]

		// data.Data = append(data.Data[:targeti], data.Data[targeti+1:]...)

		// encodedfm := data.EncodeToNum()

		// oucsv := csv.NewWriter(outfile)
		// oucsv.Comma = ' '

		// for i := 0; i < target.Length(); i++ {
		// 	entries := make([]string, 0, 10)
		// 	switch target.(type) {
		// 	case CloudForest.NumFeature:
		// 		entries = append(entries, target.GetStr(i))
		// 	case CloudForest.CatFeature:
		// 		entries = append(entries, fmt.Sprintf("%v", target.(CloudForest.CatFeature).Geti(i)))
		// 	}

		// 	for j, f := range encodedfm.Data {
		// 		v := f.(CloudForest.NumFeature).Get(i)
		// 		if v != 0.0 {
		// 			entries = append(entries, fmt.Sprintf("%v:%v", j+1, v))
		// 		}
		// 	}
		// 	//fmt.Println(entries)
		// 	err := oucsv.Write(entries)
		// 	if err != nil {
		// 		log.Fatalf("Error writing libsvm:\n%v", err)
		// 	}

		// }
		// oucsv.Flush()
		err = CloudForest.WriteLibSvm(data, *libsvmtarget, outfile)
		if err != nil {
			log.Fatalf("Error writing libsvm:\n%v", err)
		}

	}

}
예제 #3
0
파일: main.go 프로젝트: lytics/CloudForest
func main() {
	fm := flag.String("fm",
		"featurematrix.afm", "AFM formated feature matrix containing data.")

	blacklist := flag.String("blacklist",
		"", "A list of feature id's to exclude from the set of predictors.")

	targetname := flag.String("target",
		"", "The row header of the target in the feature matrix.")
	train := flag.String("train",
		"train_%v.fm", "Format string for training fms.")
	test := flag.String("test",
		"test_%v.fm", "Format string for testing fms.")

	// var zipoutput bool
	// flag.BoolVar(&zipoutput, "zip", false, "Output ziped files.")
	var unstratified bool
	flag.BoolVar(&unstratified, "unstratified", false, "Force unstratified sampeling of categorical target.")

	var writelibsvm bool
	flag.BoolVar(&writelibsvm, "writelibsvm", false, "Output libsvm.")

	var writearff bool
	flag.BoolVar(&writearff, "writearff", false, "Output arff.")

	var writeall bool
	flag.BoolVar(&writeall, "writeall", false, "Output all three formats.")

	var folds int
	flag.IntVar(&folds, "folds", 5, "Number of folds to generate.")

	var maxcats int
	flag.IntVar(&maxcats, "maxcats", -1, "Maximum number of categories to allow in a feature.")

	var impute bool
	flag.BoolVar(&impute, "impute", false, "Impute missing values to feature mean/mode.")

	var onehot bool
	flag.BoolVar(&onehot, "onehot", false, "Do one hot encoding of categorical features to boolean true false.")

	var num bool
	flag.BoolVar(&num, "num", false, "Do one hot encoding of categorical features to numerical features.")

	flag.Parse()

	//Parse Data
	data, err := CloudForest.LoadAFM(*fm)
	if err != nil {
		log.Fatal(err)
	}

	blacklisted := 0
	blacklistis := make([]bool, len(data.Data))
	if *blacklist != "" {
		fmt.Printf("Loading blacklist from: %v\n", *blacklist)
		blackfile, err := os.Open(*blacklist)
		if err != nil {
			log.Fatal(err)
		}
		tsv := csv.NewReader(blackfile)
		tsv.Comma = '\t'
		for {
			id, err := tsv.Read()
			if err == io.EOF {
				break
			} else if err != nil {
				log.Fatal(err)
			}
			if id[0] == *targetname {
				continue
			}
			i, ok := data.Map[id[0]]
			if !ok {
				fmt.Printf("Ignoring blacklist feature not found in data: %v\n", id[0])
				continue
			}
			if !blacklistis[i] {
				blacklisted += 1
				blacklistis[i] = true
			}

		}
		blackfile.Close()

	}

	newdata := make([]CloudForest.Feature, 0, len(data.Data)-blacklisted)
	newmap := make(map[string]int, len(data.Data)-blacklisted)

	for i, f := range data.Data {
		if !blacklistis[i] && (maxcats == -1 || f.NCats() <= maxcats) {
			newmap[f.GetName()] = len(newdata)
			newdata = append(newdata, f)
		}
	}

	data.Data = newdata
	data.Map = newmap

	if impute {
		fmt.Println("Imputing missing values to feature mean/mode.")
		data.ImputeMissing()
	}

	if onehot {
		fmt.Println("OneHot encoding.")
		data.OneHot()
	}

	if num {
		fmt.Println("Numerical OneHot encoding.")
		data = data.EncodeToNum()
	}

	foldis := make([][]int, 0, folds)

	foldsize := len(data.CaseLabels) / folds
	fmt.Printf("%v cases, foldsize %v\n", len(data.CaseLabels), foldsize)
	for i := 0; i < folds; i++ {
		foldis = append(foldis, make([]int, 0, foldsize))
	}

	var targetf CloudForest.Feature

	//find the target feature
	fmt.Printf("Target : %v\n", *targetname)
	targeti, ok := data.Map[*targetname]
	if !ok {
		fmt.Println("Target not found in data, doing unstratified sampeling.")
		unstratified = true
	}

	if ok {
		targetf = data.Data[targeti]

		switch targetf.(type) {
		case *CloudForest.DenseNumFeature:
			unstratified = true
		}
	}
	if unstratified {
		ncases := len(data.CaseLabels)
		cases := make([]int, ncases, ncases)
		for i := 0; i < ncases; i++ {
			cases[i] = i
		}
		CloudForest.SampleFirstN(&cases, nil, len(cases), 0)
		for j := 0; j < folds; j++ {
			for k := j * foldsize; k < (j+1)*foldsize; k++ {
				foldis[j] = append(foldis[j], cases[k])
			}
		}

	} else {
		//sample folds stratified by case
		fmt.Printf("Stratifying by %v classes.\n", targetf.(*CloudForest.DenseCatFeature).NCats())
		bSampler := CloudForest.NewBalancedSampler(targetf.(*CloudForest.DenseCatFeature))

		fmt.Printf("Stratifying by %v classes.\n", len(bSampler.Cases))
		var samples []int
		for i := 0; i < len(bSampler.Cases); i++ {
			fmt.Printf("%v cases in class %v.\n", len(bSampler.Cases[i]), i)
			//shuffle in place
			CloudForest.SampleFirstN(&bSampler.Cases[i], &samples, len(bSampler.Cases[i]), 0)
			stratFoldSize := len(bSampler.Cases[i]) / folds
			for j := 0; j < folds; j++ {
				for k := j * stratFoldSize; k < (j+1)*stratFoldSize; k++ {
					foldis[j] = append(foldis[j], bSampler.Cases[i][k])

				}
			}

		}
	}
	encode := false

	for _, f := range data.Data {
		if f.NCats() > 0 {
			encode = true
		}
	}

	encoded := data
	if encode && (writelibsvm || writeall) {
		encoded = data.EncodeToNum()
	}

	trainis := make([]int, 0, foldsize*(folds-1))
	//Write training and testing matrixes
	for i := 0; i < folds; i++ {

		trainfn := fmt.Sprintf(*train, i)
		testfn := fmt.Sprintf(*test, i)

		trainis = trainis[0:0]
		for j := 0; j < folds; j++ {
			if i != j {
				trainis = append(trainis, foldis[j]...)
			}
		}

		if writearff || writeall {
			trainW, testW := openfiles(trainfn+".arff", testfn+".arff")
			CloudForest.WriteArffCases(data, foldis[i], *targetname, testW)
			CloudForest.WriteArffCases(data, trainis, *targetname, trainW)
		}

		if ((!writelibsvm) && (!writearff)) || writeall {
			trainW, testW := openfiles(trainfn, testfn)
			data.WriteCases(testW, foldis[i])
			data.WriteCases(trainW, trainis)
		}

		if writelibsvm || writeall {
			trainW, testW := openfiles(trainfn+".libsvm", testfn+".libsvm")
			CloudForest.WriteLibSvmCases(encoded, foldis[i], *targetname, testW)
			CloudForest.WriteLibSvmCases(encoded, trainis, *targetname, trainW)
		}

		fmt.Printf("Wrote fold %v. %v testing cases and %v training cases.\n", i, len(foldis[i]), len(trainis))
	}

}
예제 #4
0
func main() {
	fm := flag.String("train",
		"featurematrix.afm", "AFM formated feature matrix containing training data.")
	rf := flag.String("rfpred",
		"", "File name to output predictor forest in sf format.")
	targetname := flag.String("target",
		"", "The row header of the target in the feature matrix.")
	imp := flag.String("importance",
		"", "File name to output importance.")
	costs := flag.String("cost",
		"", "For categorical targets, a json string to float map of the cost of falsely identifying each category.")
	dentropy := flag.String("dentropy",
		"", "Class disutilities for disutility entropy.")
	adacosts := flag.String("adacost",
		"", "Json costs for cost sentive AdaBoost.")

	rfweights := flag.String("rfweights",
		"", "For categorical targets, a json string to float map of the weights to use for each category in Weighted RF.")

	blacklist := flag.String("blacklist",
		"", "A list of feature id's to exclude from the set of predictors.")

	var nCores int
	flag.IntVar(&nCores, "nCores", 1, "The number of cores to use.")

	var StringnSamples string
	flag.StringVar(&StringnSamples, "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.")

	var StringmTry string
	flag.StringVar(&StringmTry, "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.")

	var StringleafSize string
	flag.StringVar(&StringleafSize, "leafSize", "0", "The minimum number of cases on a leaf node. If <=0 will be inferred to 1 for classification 4 for regression.")

	var maxDepth int
	flag.IntVar(&maxDepth, "maxDepth", 0, "Maximum tree depth. Ignored if 0.")

	var shuffleRE string
	flag.StringVar(&shuffleRE, "shuffleRE", "", "A regular expression to identify features that should be shuffled.")

	var blockRE string
	flag.StringVar(&blockRE, "blockRE", "", "A regular expression to identify features that should be filtered out.")

	var includeRE string
	flag.StringVar(&includeRE, "includeRE", "", "Filter features that DON'T match this RE.")

	var unlabeled string
	flag.StringVar(&unlabeled, "trans_unlabeled", "", "Class to treat as unlabeled for transduction forests.")

	var trans_alpha float64
	flag.Float64Var(&trans_alpha, "trans_alpha", 10.0, "Weight of unsupervised term in transduction impurity.")

	var trans_beta float64
	flag.Float64Var(&trans_beta, "trans_beta", 0.0, "Multiple to penalize unlabeled class by.")

	var nTrees int
	flag.IntVar(&nTrees, "nTrees", 100, "Number of trees to grow in the predictor.")

	var ace int
	flag.IntVar(&ace, "ace", 0, "Number ace permutations to do. Output ace style importance and p values.")

	var cutoff float64
	flag.Float64Var(&cutoff, "cutoff", 0.0, "P-value cutoff to apply to features for last forest after ACE.")

	var nContrasts int
	flag.IntVar(&nContrasts, "nContrasts", 0, "The number of randomized artificial contrast features to include in the feature matrix.")

	var cpuprofile = flag.String("cpuprofile", "", "write cpu profile to file")

	var contrastAll bool
	flag.BoolVar(&contrastAll, "contrastall", false, "Include a shuffled artificial contrast copy of every feature.")

	var impute bool
	flag.BoolVar(&impute, "impute", false, "Impute missing values to feature mean/mode before growth.")

	var extra bool
	flag.BoolVar(&extra, "extra", false, "Grow Extra Random Trees (supports learning from numerical variables only).")

	var splitmissing bool
	flag.BoolVar(&splitmissing, "splitmissing", false, "Split missing values onto a third branch at each node (experimental).")

	var l1 bool
	flag.BoolVar(&l1, "l1", false, "Use l1 norm regression (target must be numeric).")

	var density bool
	flag.BoolVar(&density, "density", false, "Build density estimating trees instead of classification/regression trees.")

	var vet bool
	flag.BoolVar(&vet, "vet", false, "Penalize potential splitter impurity decrease by subtracting the best split of a permuted target.")

	var positive string
	flag.StringVar(&positive, "positive", "True", "Positive class to output probabilities for.")

	var NP bool
	flag.BoolVar(&NP, "NP", false, "Do approximate Neyman-Pearson classification.")

	var NP_pos string
	flag.StringVar(&NP_pos, "NP_pos", "1", "Class label to constrain percision in NP classification.")

	var NP_a float64
	flag.Float64Var(&NP_a, "NP_a", 0.1, "Constraint on percision in NP classification [0,1]")

	var NP_k float64
	flag.Float64Var(&NP_k, "NP_k", 100, "Weight of constraint in NP classification [0,Inf+)")

	var evaloob bool
	flag.BoolVar(&evaloob, "evaloob", false, "Evaluate potential splitting features on OOB cases after finding split value in bag.")

	var force bool
	flag.BoolVar(&force, "force", false, "Force at least one non constant feature to be tested for each split.")

	var entropy bool
	flag.BoolVar(&entropy, "entropy", false, "Use entropy minimizing classification (target must be categorical).")

	var oob bool
	flag.BoolVar(&oob, "oob", false, "Calculate and report oob error.")

	var jungle bool
	flag.BoolVar(&jungle, "jungle", false, "Grow unserializable and experimental decision jungle with node recombination.")

	var caseoob string
	flag.StringVar(&caseoob, "oobpreds", "", "Calculate and report oob predictions in the file specified.")

	var progress bool
	flag.BoolVar(&progress, "progress", false, "Report tree number and running oob error.")

	var adaboost bool
	flag.BoolVar(&adaboost, "adaboost", false, "Use Adaptive boosting for regression/classification.")

	var hellinger bool
	flag.BoolVar(&hellinger, "hellinger", false, "Build trees using hellinger distance.")

	var gradboost float64
	flag.Float64Var(&gradboost, "gbt", 0.0, "Use gradient boosting with the specified learning rate.")

	var multiboost bool
	flag.BoolVar(&multiboost, "multiboost", false, "Allow multi-threaded boosting which may have unexpected results. (highly experimental)")

	var nobag bool
	flag.BoolVar(&nobag, "nobag", false, "Don't bag samples for each tree.")

	var balance bool
	flag.BoolVar(&balance, "balance", false, "Balance bagging of samples by target class for unbalanced classification.")

	var balanceby string
	flag.StringVar(&balanceby, "balanceby", "", "Roughly balanced bag the target within each class of this feature.")

	var ordinal bool
	flag.BoolVar(&ordinal, "ordinal", false, "Use ordinal regression (target must be numeric).")

	var permutate bool
	flag.BoolVar(&permutate, "permute", false, "Permute the target feature (to establish random predictive power).")

	var dotest bool
	flag.BoolVar(&dotest, "selftest", false, "Test the forest on the data and report accuracy.")

	var testfm string
	flag.StringVar(&testfm, "test", "", "Data to test the model on.")

	var scikitforest string
	flag.StringVar(&scikitforest, "scikitforest", "", "Write out a (partially complete) scikit style forest in json.")

	var noseed bool
	flag.BoolVar(&noseed, "noseed", false, "Don't seed the random number generator from time.")

	flag.Parse()

	nForest := 1

	if !noseed {
		rand.Seed(time.Now().UTC().UnixNano())
	}

	if testfm != "" {
		dotest = true
	}

	if multiboost {
		fmt.Println("MULTIBOOST!!!!1!!!!1!!11 (things may break).")
	}
	var boostMutex sync.Mutex
	boost := (adaboost || gradboost != 0.0)
	if boost && !multiboost {
		nCores = 1
	}

	if nCores > 1 {

		runtime.GOMAXPROCS(nCores)
	}
	fmt.Printf("Threads : %v\n", nCores)
	fmt.Printf("nTrees : %v\n", nTrees)
	//Parse Data
	fmt.Printf("Loading data from: %v\n", *fm)
	data, err := CloudForest.LoadAFM(*fm)
	if err != nil {
		log.Fatal(err)
	}

	if *cpuprofile != "" {
		f, err := os.Create(*cpuprofile)
		if err != nil {
			log.Fatal(err)
		}
		pprof.StartCPUProfile(f)
		defer pprof.StopCPUProfile()
	}

	if nContrasts > 0 {
		fmt.Printf("Adding %v Random Contrasts\n", nContrasts)
		data.AddContrasts(nContrasts)
	}
	if contrastAll {
		fmt.Printf("Adding Random Contrasts for All Features.\n")
		data.ContrastAll()
	}

	blacklisted := 0
	blacklistis := make([]bool, len(data.Data))
	if *blacklist != "" {
		fmt.Printf("Loading blacklist from: %v\n", *blacklist)
		blackfile, err := os.Open(*blacklist)
		if err != nil {
			log.Fatal(err)
		}
		tsv := csv.NewReader(blackfile)
		tsv.Comma = '\t'
		for {
			id, err := tsv.Read()
			if err == io.EOF {
				break
			} else if err != nil {
				log.Fatal(err)
			}
			i, ok := data.Map[id[0]]
			if !ok {
				fmt.Printf("Ignoring blacklist feature not found in data: %v\n", id[0])
				continue
			}
			if !blacklistis[i] {
				blacklisted += 1
				blacklistis[i] = true
			}

		}
		blackfile.Close()

	}

	//find the target feature
	fmt.Printf("Target : %v\n", *targetname)
	targeti, ok := data.Map[*targetname]
	if !ok {
		log.Fatal("Target not found in data.")
	}

	if blockRE != "" {
		re := regexp.MustCompile(blockRE)
		for i, feature := range data.Data {
			if targeti != i && re.MatchString(feature.GetName()) {
				if blacklistis[i] == false {
					blacklisted += 1
					blacklistis[i] = true
				}

			}

		}

	}

	if includeRE != "" {
		re := regexp.MustCompile(includeRE)
		for i, feature := range data.Data {
			if targeti != i && !re.MatchString(feature.GetName()) {
				if blacklistis[i] == false {
					blacklisted += 1
					blacklistis[i] = true
				}

			}

		}
	}

	nFeatures := len(data.Data) - blacklisted - 1
	fmt.Printf("Non Target Features : %v\n", nFeatures)

	mTry := CloudForest.ParseAsIntOrFractionOfTotal(StringmTry, nFeatures)
	if mTry <= 0 {

		mTry = int(math.Ceil(math.Sqrt(float64(nFeatures))))
	}
	fmt.Printf("mTry : %v\n", mTry)

	if impute {
		fmt.Println("Imputing missing values to feature mean/mode.")
		data.ImputeMissing()
	}

	if permutate {
		fmt.Println("Permuting target feature.")
		data.Data[targeti].Shuffle()
	}

	if shuffleRE != "" {
		re := regexp.MustCompile(shuffleRE)
		shuffled := 0
		for i, feature := range data.Data {
			if targeti != i && re.MatchString(feature.GetName()) {
				data.Data[i].Shuffle()
				shuffled += 1

			}

		}
		fmt.Printf("Shuffled %v features matching %v\n", shuffled, shuffleRE)
	}

	targetf := data.Data[targeti]
	unboostedTarget := targetf.Copy()

	var bSampler CloudForest.Bagger
	if balance {
		bSampler = CloudForest.NewBalancedSampler(targetf.(*CloudForest.DenseCatFeature))
	}

	if balanceby != "" {
		bSampler = CloudForest.NewSecondaryBalancedSampler(targetf.(*CloudForest.DenseCatFeature), data.Data[data.Map[balanceby]].(*CloudForest.DenseCatFeature))
		balance = true

	}

	nNonMissing := 0

	for i := 0; i < targetf.Length(); i++ {
		if !targetf.IsMissing(i) {
			nNonMissing += 1
		}

	}
	fmt.Printf("non-missing cases: %v\n", nNonMissing)

	leafSize := CloudForest.ParseAsIntOrFractionOfTotal(StringleafSize, nNonMissing)

	if leafSize <= 0 {
		if boost {
			leafSize = nNonMissing / 3
		} else if targetf.NCats() == 0 {
			//regression
			leafSize = 4
		} else {
			//classification
			leafSize = 1
		}
	}
	fmt.Printf("leafSize : %v\n", leafSize)

	//infer nSamples and mTry from data if they are 0
	nSamples := CloudForest.ParseAsIntOrFractionOfTotal(StringnSamples, nNonMissing)
	if nSamples <= 0 {
		nSamples = nNonMissing
	}
	fmt.Printf("nSamples : %v\n", nSamples)

	if progress {
		oob = true
	}
	if caseoob != "" {
		oob = true
	}
	var oobVotes CloudForest.VoteTallyer
	if oob {
		fmt.Println("Recording oob error.")
		if targetf.NCats() == 0 {
			//regression
			oobVotes = CloudForest.NewNumBallotBox(data.Data[0].Length())
		} else {
			//classification
			oobVotes = CloudForest.NewCatBallotBox(data.Data[0].Length())
		}
	}

	//****** Set up Target for Alternative Impurity  if needed *******//
	var target CloudForest.Target
	if density {
		fmt.Println("Estimating Density.")
		target = &CloudForest.DensityTarget{&data.Data, nNonMissing}
	} else {

		switch targetf.(type) {

		case CloudForest.NumFeature:
			fmt.Println("Performing regression.")
			if l1 {
				fmt.Println("Using l1/absolute deviance error.")
				targetf = &CloudForest.L1Target{targetf.(CloudForest.NumFeature)}
			}
			if ordinal {
				fmt.Println("Using Ordinal (mode) prediction.")
				targetf = CloudForest.NewOrdinalTarget(targetf.(CloudForest.NumFeature))
			}
			switch {
			case gradboost != 0.0:
				fmt.Println("Using Gradient Boosting.")
				targetf = CloudForest.NewGradBoostTarget(targetf.(CloudForest.NumFeature), gradboost)

			case adaboost:
				fmt.Println("Using Numeric Adaptive Boosting.")
				targetf = CloudForest.NewNumAdaBoostTarget(targetf.(CloudForest.NumFeature))
			}
			target = targetf

		case CloudForest.CatFeature:
			fmt.Printf("Performing classification with %v categories.\n", targetf.NCats())
			switch {
			case NP:
				fmt.Printf("Performing Approximate Neyman-Pearson Classification with constrained false \"%v\".\n", NP_pos)
				fmt.Printf("False %v constraint: %v, constraint weight: %v.\n", NP_pos, NP_a, NP_k)
				targetf = CloudForest.NewNPTarget(targetf.(CloudForest.CatFeature), NP_pos, NP_a, NP_k)
			case *costs != "":
				fmt.Println("Using misclassification costs: ", *costs)
				costmap := make(map[string]float64)
				err := json.Unmarshal([]byte(*costs), &costmap)
				if err != nil {
					log.Fatal(err)
				}

				regTarg := CloudForest.NewRegretTarget(targetf.(CloudForest.CatFeature))
				regTarg.SetCosts(costmap)
				targetf = regTarg
			case *dentropy != "":
				fmt.Println("Using entropy with disutilities: ", *dentropy)
				costmap := make(map[string]float64)
				err := json.Unmarshal([]byte(*dentropy), &costmap)
				if err != nil {
					log.Fatal(err)
				}

				deTarg := CloudForest.NewDEntropyTarget(targetf.(CloudForest.CatFeature))
				deTarg.SetCosts(costmap)
				targetf = deTarg
			case *adacosts != "":
				fmt.Println("Using cost sensative AdaBoost costs: ", *adacosts)
				costmap := make(map[string]float64)
				err := json.Unmarshal([]byte(*adacosts), &costmap)
				if err != nil {
					log.Fatal(err)
				}

				actarget := CloudForest.NewAdaCostTarget(targetf.(CloudForest.CatFeature))
				actarget.SetCosts(costmap)
				targetf = actarget

			case *rfweights != "":
				fmt.Println("Using rf weights: ", *rfweights)
				weightmap := make(map[string]float64)
				err := json.Unmarshal([]byte(*rfweights), &weightmap)
				if err != nil {
					log.Fatal(err)
				}

				wrfTarget := CloudForest.NewWRFTarget(targetf.(CloudForest.CatFeature), weightmap)
				targetf = wrfTarget

			case entropy:
				fmt.Println("Using entropy minimization.")
				targetf = &CloudForest.EntropyTarget{targetf.(CloudForest.CatFeature)}

			case adaboost:

				fmt.Println("Using Adaptive Boosting.")
				targetf = CloudForest.NewAdaBoostTarget(targetf.(CloudForest.CatFeature))

			case hellinger:
				fmt.Println("Using Hellinger Distance with postive class:", positive)
				targetf = CloudForest.NewHDistanceTarget(targetf.(CloudForest.CatFeature), positive)

			case gradboost != 0.0:
				fmt.Println("Using Gradient Boosting Classification with postive class:", positive)
				targetf = CloudForest.NewGradBoostClassTarget(targetf.(CloudForest.CatFeature), gradboost, positive)

			}

			if unlabeled != "" {
				fmt.Println("Using traduction forests with unlabeled class: ", unlabeled)
				targetf = CloudForest.NewTransTarget(targetf.(CloudForest.CatFeature), &data.Data, unlabeled, trans_alpha, trans_beta, nNonMissing)

			}
			target = targetf

		}
	}

	var forestwriter *CloudForest.ForestWriter
	if *rf != "" {
		forestfile, err := os.Create(*rf)
		if err != nil {
			log.Fatal(err)
		}
		defer forestfile.Close()
		forestwriter = CloudForest.NewForestWriter(forestfile)
		switch target.(type) {
		case CloudForest.TargetWithIntercept:
			forestwriter.WriteForestHeader(0, *targetname, target.(CloudForest.TargetWithIntercept).Intercept())
		}
	}
	//****************** Setup For ACE ********************************//
	var aceImps [][]float64
	firstace := len(data.Data)

	if ace > 0 {

		fmt.Printf("Performing ACE analysis with %v forests/permutations.\n", ace)

		data.ContrastAll()

		for i := 0; i < firstace; i++ {
			blacklistis = append(blacklistis, blacklistis[i])
		}
		blacklistis[targeti+firstace] = true

		aceImps = make([][]float64, len(data.Data))
		for i := 0; i < len(data.Data); i++ {
			aceImps[i] = make([]float64, ace)
		}
		nForest = ace
		if cutoff > 0 {
			nForest++
		}
	}

	//****************** Needed Collections and vars ******************//
	var trees []*CloudForest.Tree
	trees = make([]*CloudForest.Tree, 0, nTrees)

	var imppnt *[]*CloudForest.RunningMean
	var mmdpnt *[]*CloudForest.RunningMean
	if *imp != "" {
		fmt.Println("Recording Importance Scores.")

		imppnt = CloudForest.NewRunningMeans(len(data.Data))
		mmdpnt = CloudForest.NewRunningMeans(len(data.Data))
	} else if ace > 0 {
		imppnt = CloudForest.NewRunningMeans(len(data.Data))
	}

	var scikikittrees []CloudForest.ScikitTree

	if scikitforest != "" {
		scikikittrees = make([]CloudForest.ScikitTree, 0, nTrees)
	}

	//****************** Good Stuff Stars Here ;) ******************//

	trainingStart := time.Now()

	for foresti := 0; foresti < nForest; foresti++ {
		var treesStarted, treesFinished int
		treesStarted = nCores
		var recordingTree sync.Mutex
		var waitGroup sync.WaitGroup

		waitGroup.Add(nCores)
		treechan := make(chan *CloudForest.Tree, 0)
		//fmt.Println("forest ", foresti)
		//Grow a single forest on nCores
		for core := 0; core < nCores; core++ {

			grow := func() {
				weight := -1.0
				canidates := make([]int, 0, len(data.Data))
				for i := 0; i < len(data.Data); i++ {
					if i != targeti && !blacklistis[i] {
						canidates = append(canidates, i)
					}
				}

				tree := CloudForest.NewTree()
				tree.Target = *targetname
				cases := make([]int, 0, nNonMissing)
				oobcases := make([]int, 0, nNonMissing)

				if nobag {
					for i := 0; i < nNonMissing; i++ {
						if !targetf.IsMissing(i) {
							cases = append(cases, i)
						}
					}
				}

				var depthUsed *[]int
				if mmdpnt != nil {
					du := make([]int, len(data.Data))
					depthUsed = &du
				}

				allocs := CloudForest.NewBestSplitAllocs(nSamples, targetf)
				for {
					nCases := data.Data[0].Length()
					//sample nCases case with replacement
					if !nobag {
						cases = cases[0:0]

						if balance {
							bSampler.Sample(&cases, nSamples)

						} else {
							for j := 0; len(cases) < nSamples; j++ {
								r := rand.Intn(nCases)
								if !targetf.IsMissing(r) {
									cases = append(cases, r)
								}
							}
						}

					}

					if nobag && nSamples != nCases {
						cases = cases[0:0]
						for i := 0; i < nCases; i++ {
							if !targetf.IsMissing(i) {
								cases = append(cases, i)
							}
						}
						CloudForest.SampleFirstN(&cases, &cases, nSamples, 0)

					}

					if oob || evaloob {
						ibcases := make([]bool, nCases)
						for _, v := range cases {
							ibcases[v] = true
						}
						oobcases = oobcases[0:0]
						for i, v := range ibcases {
							if !v {
								oobcases = append(oobcases, i)
							}
						}
					}

					if jungle {
						tree.GrowJungle(data, target, cases, canidates, oobcases, mTry, leafSize, maxDepth, splitmissing, force, vet, evaloob, extra, imppnt, depthUsed, allocs)

					} else {
						tree.Grow(data, target, cases, canidates, oobcases, mTry, leafSize, maxDepth, splitmissing, force, vet, evaloob, extra, imppnt, depthUsed, allocs)
					}
					if mmdpnt != nil {
						for i, v := range *depthUsed {
							if v != 0 {
								(*mmdpnt)[i].Add(float64(v))
								(*depthUsed)[i] = 0
							}

						}
					}

					if boost {
						boostMutex.Lock()
						ls, ps := tree.Partition(data)
						weight = targetf.(CloudForest.BoostingTarget).Boost(ls, ps)
						boostMutex.Unlock()
						if weight == math.Inf(1) {
							fmt.Printf("Boosting Reached Weight of %v\n", weight)
							close(treechan)
							break
						}

						tree.Weight = weight
					}

					if oob && foresti == nForest-1 {
						tree.VoteCases(data, oobVotes, oobcases)
					}

					////////////// Lock mutext to ouput tree ////////
					if nCores > 1 {
						recordingTree.Lock()
					}

					if forestwriter != nil && foresti == nForest-1 {
						forestwriter.WriteTree(tree, treesFinished)
					}

					if scikitforest != "" {
						skt := CloudForest.NewScikitTree(nFeatures)
						CloudForest.BuildScikitTree(0, tree.Root, skt)
						scikikittrees = append(scikikittrees, *skt)
					}

					if dotest && foresti == nForest-1 {
						trees = append(trees, tree)

						if treesStarted < nTrees-1 {
							//newtree := new(CloudForest.Tree)
							tree = CloudForest.NewTree()
							tree.Target = *targetname
						}
					}
					if progress {
						treesFinished++
						fmt.Printf("Model oob error after tree %v : %v\n", treesFinished, oobVotes.TallyError(unboostedTarget))
					}
					if treesStarted < nTrees {
						treesStarted++
					} else {
						if nCores > 1 {
							recordingTree.Unlock()
							waitGroup.Done()
						}
						break

					}
					if nCores > 1 {
						recordingTree.Unlock()
					}
					//////// Unlock //////////////////////////
					// treechan <- tree
					// tree = <-treechan
				}
			}

			if nCores > 1 {
				go grow()
			} else {
				grow()
			}

		}
		if nCores > 1 {
			waitGroup.Wait()
		}
		// for i := 0; i < nTrees; i++ {
		// 	tree := <-treechan
		// 	if tree == nil {
		// 		break
		// 	}
		// 	if forestwriter != nil && foresti == nForest-1 {
		// 		forestwriter.WriteTree(tree, i)
		// 	}

		// 	if dotest && foresti == nForest-1 {
		// 		trees = append(trees, tree)

		// 		if i < nTrees-1 {
		// 			//newtree := new(CloudForest.Tree)
		// 			treechan <- CloudForest.NewTree()
		// 		}
		// 	} else {
		// 		if i < nTrees-1 {
		// 			treechan <- tree
		// 		}
		// 	}
		// 	if progress {
		// 		fmt.Printf("Model oob error after tree %v : %v\n", i, oobVotes.TallyError(unboostedTarget))
		// 	}

		// }
		//Single forest growth is over.

		//Record importance scores from this forest for ace
		if ace > 0 && (cutoff == 0.0 || foresti < nForest-1) {
			if foresti < nForest-1 {
				fmt.Printf("Finished ACE forest %v.\n", foresti)
			}
			//Record Importance scores
			for i := 0; i < len(data.Data); i++ {
				mean, count := (*imppnt)[i].Read()
				aceImps[i][foresti] = mean * float64(count) / float64(nTrees)
			}

			//Reset importance scores
			imppnt = CloudForest.NewRunningMeans(len(data.Data))

			//Reshuffle contrast features
			for i := firstace; i < len(data.Data); i++ {
				if !blacklistis[i] {
					data.Data[i].Shuffle()
				}
			}

			if cutoff > 0 && foresti == nForest-2 {
				sigcount := 0
				for i := range blacklistis {

					if i < firstace && !blacklistis[i] {
						p, _, _, m := stats.Ttest(&aceImps[i], &aceImps[i+firstace])
						if p < cutoff && m > 0.0 && i != targeti {
							blacklistis[i] = false
							sigcount++
						} else {
							blacklistis[i] = true
						}
					}
					if i >= firstace {
						blacklistis[i] = true
					}

				}
				mTry = CloudForest.ParseAsIntOrFractionOfTotal(StringmTry, sigcount)
				if mTry <= 0 {

					mTry = int(math.Ceil(math.Sqrt(float64(sigcount))))
				}
				fmt.Printf("Growing non-ACE forest with %v features with p-value < %v.\nmTry: %v\n", sigcount, cutoff, mTry)
			}
		}
	}

	trainingEnd := time.Now()
	fmt.Printf("Total training time (seconds): %v\n", trainingEnd.Sub(trainingStart).Seconds())

	if scikitforest != "" {
		skfile, err := os.Create(scikitforest)
		if err != nil {
			log.Fatal(err)
		}
		defer skfile.Close()
		skencoder := json.NewEncoder(skfile)
		err = skencoder.Encode(scikikittrees)
		if err != nil {
			log.Fatal(err)
		}
	}

	if oob {
		fmt.Printf("Out of Bag Error : %v\n", oobVotes.TallyError(unboostedTarget))
	}
	if caseoob != "" {
		caseoobfile, err := os.Create(caseoob)
		if err != nil {
			log.Fatal(err)
		}
		defer caseoobfile.Close()
		for i := 0; i < unboostedTarget.Length(); i++ {
			fmt.Fprintf(caseoobfile, "%v\t%v\t%v\n", data.CaseLabels[i], oobVotes.Tally(i), unboostedTarget.GetStr(i))
		}
	}

	if *imp != "" {

		impfile, err := os.Create(*imp)
		if err != nil {
			log.Fatal(err)
		}
		defer impfile.Close()
		if ace > 0 {

			for i := 0; i < firstace; i++ {

				p, _, _, m := stats.Ttest(&aceImps[i], &aceImps[i+firstace])

				fmt.Fprintf(impfile, "%v\t%v\t%v\t%v\n", *targetname, data.Data[i].GetName(), p, m)

			}
		} else {
			//Write standard importance file
			for i, v := range *imppnt {
				mean, count := v.Read()
				meanMinDepth, treeCount := (*mmdpnt)[i].Read()
				fmt.Fprintf(impfile, "%v\t%v\t%v\t%v\t%v\t%v\t%v\n", data.Data[i].GetName(), mean, count, mean*float64(count)/float64(nTrees), mean*float64(count)/float64(treeCount), treeCount, meanMinDepth)

			}
		}
	}

	if dotest {
		var bb CloudForest.VoteTallyer

		testdata := data
		testtarget := unboostedTarget
		if testfm != "" {
			var err error
			testdata, err = CloudForest.LoadAFM(testfm)
			if err != nil {
				log.Fatal(err)
			}
			targeti, ok = testdata.Map[*targetname]
			if !ok {
				log.Fatal("Target not found in test data.")
			}
			testtarget = testdata.Data[targeti]

			for _, tree := range trees {

				tree.StripCodes()

			}
		}

		if unboostedTarget.NCats() == 0 {
			//regression
			bb = CloudForest.NewNumBallotBox(testdata.Data[0].Length())
		} else {
			//classification
			bb = CloudForest.NewCatBallotBox(testdata.Data[0].Length())
		}

		for _, tree := range trees {
			tree.Vote(testdata, bb)
		}

		fmt.Printf("Error: %v\n", bb.TallyError(testtarget))

		if testtarget.NCats() != 0 {
			falsesbypred := make([]int, testtarget.NCats())
			predtotals := make([]int, testtarget.NCats())

			truebytrue := make([]int, testtarget.NCats())
			truetotals := make([]int, testtarget.NCats())

			correct := 0
			nas := 0
			length := testtarget.Length()
			for i := 0; i < length; i++ {
				truei := testtarget.(*CloudForest.DenseCatFeature).Geti(i)
				truetotals[truei]++
				pred := bb.Tally(i)
				if pred == "NA" {
					nas++
				} else {
					predi := testtarget.(*CloudForest.DenseCatFeature).CatToNum(pred)
					predtotals[predi]++
					if pred == testtarget.GetStr(i) {
						correct++
						truebytrue[truei]++
					} else {

						falsesbypred[predi]++
					}
				}

			}
			fmt.Printf("Classified: %v / %v = %v\n", correct, length, float64(correct)/float64(length))
			for i, v := range testtarget.(*CloudForest.DenseCatFeature).Back {
				fmt.Printf("Label %v Percision (Actuall/Predicted): %v / %v = %v\n", v, falsesbypred[i], predtotals[i], float64(falsesbypred[i])/float64(predtotals[i]))
				falses := truetotals[i] - truebytrue[i]
				fmt.Printf("Label %v Missed/Actuall Rate: %v / %v = %v\n", v, falses, truetotals[i], float64(falses)/float64(truetotals[i]))

			}
			if nas != 0 {
				fmt.Printf("Couldn't predict %v cases due to missing values.\n", nas)
			}
		}

	}

}
예제 #5
0
func main() {
	fm := flag.String("fm", "featurematrix.afm", "AFM formated feature matrix to use.")
	rf := flag.String("rfpred", "rface.sf", "A predictor forest.")
	outf := flag.String("leaves", "leaves.tsv", "a case by case sparse matrix of leaf co-occurrence in tsv format")
	boutf := flag.String("branches", "", "a case by feature sparse matrix of leaf co-occurrence in tsv format")
	soutf := flag.String("splits", "", "a file to write a json record of splite per feature")
	var threads int
	flag.IntVar(&threads, "threads", 1, "Parse seperate forests in n seperate threads.")

	flag.Parse()

	splits := make(map[string][]string)

	//Parse Data
	data, err := CloudForest.LoadAFM(*fm)
	if err != nil {
		log.Fatal(err)
	}

	log.Print("Data file ", len(data.Data), " by ", data.Data[0].Length())

	counts := new(CloudForest.SparseCounter)
	var caseFeatureCounts *CloudForest.SparseCounter
	if *boutf != "" {
		caseFeatureCounts = new(CloudForest.SparseCounter)
	}

	files := strings.Split(*rf, ",")

	runtime.GOMAXPROCS(threads)

	fileChan := make(chan string, 0)
	doneChan := make(chan int, 0)

	go func() {
		for _, fn := range files {
			fileChan <- fn
		}
	}()

	for i := 0; i < threads; i++ {

		go func() {
			for {
				fn := <-fileChan

				forestfile, err := os.Open(fn) // For read access.
				if err != nil {
					log.Fatal(err)
				}
				defer forestfile.Close()
				forestreader := CloudForest.NewForestReader(forestfile)
				forest, err := forestreader.ReadForest()
				if err != nil {
					log.Fatal(err)
				}
				log.Print("Forest has ", len(forest.Trees), " trees ")

				for i := 0; i < len(forest.Trees); i++ {
					fmt.Print(".")
					leaves := forest.Trees[i].GetLeaves(data, caseFeatureCounts)
					for _, leaf := range leaves {
						for j := 0; j < len(leaf.Cases); j++ {
							for k := 0; k < len(leaf.Cases); k++ {

								counts.Add(leaf.Cases[j], leaf.Cases[k], 1)

							}
						}
					}

					if *soutf != "" {
						forest.Trees[i].Root.Climb(func(n *CloudForest.Node) {
							if n.Splitter != nil {
								name := n.Splitter.Feature
								_, ok := splits[name]
								if !ok {
									splits[name] = make([]string, 0, 10)
								}
								split := ""
								switch n.Splitter.Numerical {
								case true:
									split = fmt.Sprintf("%v", n.Splitter.Value)
								case false:
									keys := make([]string, 0, len(n.Splitter.Left))
									for k := range n.Splitter.Left {
										keys = append(keys, k)
									}
									split = strings.Join(keys, ",")
								}
								splits[name] = append(splits[name], split)
							}
						})
					}

				}
				doneChan <- 1
			}
		}()

	}

	for i := 0; i < len(files); i++ {
		<-doneChan
	}

	log.Print("Outputting Case Case  Co-Occurrence Counts")
	outfile, err := os.Create(*outf)
	if err != nil {
		log.Fatal(err)
	}
	defer outfile.Close()
	counts.WriteTsv(outfile)

	if *boutf != "" {
		log.Print("Outputting Case Feature Co-Occurrence Counts")
		boutfile, err := os.Create(*boutf)
		if err != nil {
			log.Fatal(err)
		}
		defer boutfile.Close()
		caseFeatureCounts.WriteTsv(boutfile)
	}

	if *soutf != "" {
		soutfile, err := os.Create(*soutf)
		if err != nil {
			log.Fatal(err)
		}
		defer soutfile.Close()
		encoder := json.NewEncoder(soutfile)
		encoder.Encode(splits)
	}
}