R help - Apr 2018 - xgboost: problems with predictions for count data [SEC=UNCLASSIFIED]

Hi All,

I tried to use xgboost to model and predict count data. The predictions are
however not as expected as shown below.
# sponge count data in library(spm)
    library(spm)
data(sponge)
data(sponge.grid)
names(sponge)
[1] "easting"  "northing" "sponge"  
"tpi3"     "var7"     "entro7"   "bs34" 
"bs11"
names(sponge.grid)
[1] "easting"  "northing" "tpi3"    
"var7"     "entro7"   "bs34"     "bs11"
    range(sponge[, c(3)])
[1]  1 39 # count sample data

# the expected predictions are:
set.seed(1234)
gbmpred1 <- gbmpred(sponge[, -c(3)], sponge[, 3], sponge.grid[, c(1:2)],
sponge.grid, family = "poisson", n.cores=2)
range(gbmpred1$Predictions)
[1] 10.04643 31.39230 # the expected predictions

# Here are results from xgboost
# use count:poisson
library(xgboost)
    xgbst2.1 <- xgboost(data = as.matrix(sponge[, -c(3)]), label = sponge[,
3], max_depth = 2, eta = 0.001, nthread = 6, nrounds = 3000, objective =
"count:poisson")
    xgbstpred2 <- predict(xgbst2.1, as.matrix(sponge.grid))
head(xgbstpred2)
range(xgbstpred2)
[1] 1.109032 4.083049 # much lower than expected
    table(xgbstpred2)
                1.10903215408325 1.26556181907654   3.578040599823
4.08304929733276  # only four predictions, why?
                36535             2714            40930            15351

   plot(gbmpred1$Predictions, xgbstpred2) # Fig 1

   # use reg:linear
    xgbst2.2 <- xgboost(data = as.matrix(sponge[, -c(3)]), label = sponge[,
3], max_depth = 2, eta = 0.001, nthread = 6, nrounds = 3000, objective =
"reg:linear")
    xgbstpred2.2 <- predict(xgbst2.2, as.matrix(sponge.grid))
    head(xgbstpred2.2)
    table(xgbstpred2.2)
    range( xgbstpred2.2)
[1]  9.019174 23.060669 # this is much closer to but still lower than what
expected

   plot(gbmpred1$Predictions, xgbstpred2.2) # Fig 2

# use count:poisson and subsample = 0.5
set.seed(1234)
    param <- list(max_depth = 2, eta = 0.001, gamma = 0.001, subsample = 0.5,
silent = 1, nthread = 6, objective = "count:poisson")
    xgbst2.4 <- xgboost(data = as.matrix(sponge[, -c(3)]), label = sponge[,
3], params = param, nrounds = 3000)
    xgbstpred2.4 <- predict(xgbst2.4, as.matrix(sponge.grid))
    head(xgbstpred2.4)
    table(xgbstpred2.4)
    range(xgbstpred2.4)
[1] 1.188561 3.986767 # this is much lower than what expected

   plot(gbmpred1$Predictions, xgbstpred2.4) # Fig 3
  plot(xgbstpred2.2, xgbstpred2.4) # Fig 4

All these were run in R 3.3.3 on Windows"
> Sys.info()
                     sysname                      release
                   "Windows"                      "7 x64"
                     version
"build 7601, Service Pack 1"
                     machine
                    "x86-64"

Have I miss-specified or missed some parameters? Or there is a bug in xgboost. I
am grateful for any help.

Kind regards,
Jin

Jin Li, PhD | Spatial Modeller / Computational Statistician
National Earth and Marine Observations | Environmental Geoscience Division
t:  +61 2 6249 9899    www.ga.gov.au<http://www.ga.gov.au/>

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