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pharynx

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ARFF
Publicly available Visibility: public Uploaded 23-04-2014 by Jan van Rijn

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Please cite:
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Case number deleted.
As used by Kilpatrick, D. & Cameron-Jones, M. (1998). Numeric prediction
using instance-based learning with encoding length selection. In Progress
in Connectionist-Based Information Systems. Singapore: Springer-Verlag.
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Name: Pharynx (A clinical Trial in the Trt. of Carcinoma of the Oropharynx).
SIZE: 195 observations, 13 variables.
DESCRIPTIVE ABSTRACT:
The .dat file gives the data for a part of a large clinical trial
carried out by the Radiation Therapy Oncology Group in the United States.
The full study included patients with squamous carcinoma of 15 sites in
the mouth and throat, with 16 participating institutions, though only data
on three sites in the oropharynx reported by the six largest institutions
are considered here. Patients entering the study were randomly assigned to
one of two treatment groups, radiation therapy alone or radiation therapy
together with a chemotherapeutic agent. One objective of the study was to
compare the two treatment policies with respect to patient survival.
SOURCE: The Statistical Analysis of Failure Time Data, by JD Kalbfleisch
& RL Prentice, (1980), Published by John Wiley & Sons
VARIABLE DESCRIPTIONS:
The data are in free format. That is, at least one blank space separates
each variable in the .dat file. The variables are as follows:
Case: Case Number
Inst: Participating Institution
sex: 1=male, 2=female
Treatment: 1=standard, 2=test
Grade: 1=well differentiated, 2=moderately differentiated,
3=poorly differentiated, 9=missing
Age: In years at time of diagnosis
Condition: 1=no disability, 2=restricted work, 3=requires assistance with
self care, 4=bed confined, 9=missing
Site: 1=faucial arch, 2=tonsillar fossa, 3=posterior pillar,
4=pharyngeal tongue, 5=posterior wall
T staging: 1=primary tumor measuring 2 cm or less in largest diameter,
2=primary tumor measuring 2 cm to 4 cm in largest diameter with
minimal infiltration in depth, 3=primary tumor measuring more
than 4 cm, 4=massive invasive tumor
N staging: 0=no clinical evidence of node metastases, 1=single positive
node 3 cm or less in diameter, not fixed, 2=single positive
node more than 3 cm in diameter, not fixed, 3=multiple
positive nodes or fixed positive nodes
Entry Date: Date of study entry: Day of year and year
Status: 0=censored, 1=dead
Time: Survival time in days from day of diagnosis
STORY BEHIND THE DATA:
Approximately 30% of the survival times are censored owing primarily to
patients surviving to the time of analysis. Some patients were lost
to follow-up because the patient moved or transferred to an institution not
participating in the study, though these cases were relatively rare. From
a statistical point of view, an important feature of these data is the
considerable lack of homogeneity between individuals being studied.
Of course, as part of the study design, certain criteria for patient
eligibility had to be met which eliminated extremes in the extent of disease,
but still many factors are not controlled.
This study included measurements of many covariates which would be expected
to relate to survival experience. Six such variables are given in the data
(sex, T staging, N staging, age, general condition, and grade). The site
of the primary tumor and possible differences between participating
institutions require consideration as well.
The T,N staging classification gives a measure of the extent of the tumor at
the primary site and at regional lymph nodes. T=1, refers to a small primary
tumor, 2 centimeters or less in largest diameter, whereas T=4 is a massive
tumor with extension to adjoining tissue. T=2 and T=3 refer to intermediate
cases. N=0 refers to there being no clinical evidence of a lymph node
metastasis and N=1, N=2, N=3 indicate, in increasing magnitude, the extent of
existing lymph node involvement. Patients with classifications T=1,N=0;
T=1,N=1; T=2,N=0; or T=2,N=1, or with distant metastases were excluded
from study.
The variable general condition gives a measure of the functional capacity of
the patient at the time of diagnosis (1 refers to no disability whereas
4 denotes bed confinement; 2 and 3 measure intermediate levels). The variable
grade is a measure of the degree of differentiation of the tumor (the degree
to which the tumor cell resembles the host cell) from 1 (well differentiated)
to 3 (poorly differentiated)
In addition to the primary question whether the combined treatment mode is
preferable to the conventional radiation therapy, it is of considerable
interest to determine the extent to which the several covariates relate to
subsequent survival. It is also imperative in answering the primary question
to adjust the survivals for possible imbalance that may be present in the
study with regard to the other covariates. Such problems are similar to those
encountered in the classical theory of linear regression and the analysis of
covariance. Again, the need to accommodate censoring is an important
distinguishing point. In many situations it is also important to develop
nonparametric and robust procedures since there is frequently little empirical
or theoretical work to support a particular family of failure time
distributions.

class (target) | numeric | 177 unique values 0 missing | |

Inst | nominal | 6 unique values 0 missing | |

sex | nominal | 2 unique values 0 missing | |

Treatment | nominal | 2 unique values 0 missing | |

Grade | nominal | 3 unique values 1 missing | |

Age | numeric | 48 unique values 0 missing | |

Condition | nominal | 5 unique values 1 missing | |

Site | nominal | 3 unique values 0 missing | |

T | nominal | 4 unique values 0 missing | |

N | nominal | 4 unique values 0 missing | |

Entry (ignore) | nominal | 184 unique values 0 missing | |

Status | nominal | 2 unique values 0 missing |

An estimate of the amount of irrelevant information in the attributes regarding the class. Equals (MeanAttributeEntropy - MeanMutualInformation) divided by MeanMutualInformation.

First quartile of mutual information between the nominal attributes and the target attribute.

Kappa coefficient achieved by the landmarker weka.classifiers.bayes.NaiveBayes -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Kappa coefficient achieved by the landmarker weka.classifiers.trees.RandomTree -depth 3

21.5

Average number of distinct values among the attributes of the nominal type.

-0.03

First quartile of skewness among attributes of the numeric type.

Area Under the ROC Curve achieved by the landmarker weka.classifiers.lazy.IBk -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

57.11

Standard deviation of the number of distinct values among attributes of the nominal type.

11.22

First quartile of standard deviation of attributes of the numeric type.

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.REPTree -L 2

Error rate achieved by the landmarker weka.classifiers.lazy.IBk -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Kappa coefficient achieved by the landmarker weka.classifiers.lazy.IBk -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

0.33

Second quartile (Median) of kurtosis among attributes of the numeric type.

309.58

Second quartile (Median) of means among attributes of the numeric type.

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.REPTree -L 3

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.DecisionStump

Second quartile (Median) of mutual information between the nominal attributes and the target attribute.

Minimal mutual information between the nominal attributes and the target attribute.

0.52

Second quartile (Median) of skewness among attributes of the numeric type.

Kappa coefficient achieved by the landmarker weka.classifiers.trees.DecisionStump

2

The minimal number of distinct values among attributes of the nominal type.

214.97

Second quartile (Median) of standard deviation of attributes of the numeric type.

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.RandomTree -depth 1

Maximum mutual information between the nominal attributes and the target attribute.

Error rate achieved by the landmarker weka.classifiers.trees.RandomTree -depth 1

Number of attributes needed to optimally describe the class (under the assumption of independence among attributes). Equals ClassEntropy divided by MeanMutualInformation.

184

The maximum number of distinct values among attributes of the nominal type.

0.37

Third quartile of kurtosis among attributes of the numeric type.

Kappa coefficient achieved by the landmarker weka.classifiers.trees.RandomTree -depth 1

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.J48 -C .00001

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.DecisionStump -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.RandomTree -depth 2

Third quartile of mutual information between the nominal attributes and the target attribute.

Error rate achieved by the landmarker weka.classifiers.trees.DecisionStump -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Error rate achieved by the landmarker weka.classifiers.trees.RandomTree -depth 2

1.06

Third quartile of skewness among attributes of the numeric type.

Kappa coefficient achieved by the landmarker weka.classifiers.trees.DecisionStump -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Kappa coefficient achieved by the landmarker weka.classifiers.trees.RandomTree -depth 2

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.J48 -C .0001

0.28

First quartile of kurtosis among attributes of the numeric type.

418.72

Third quartile of standard deviation of attributes of the numeric type.

Area Under the ROC Curve achieved by the landmarker weka.classifiers.bayes.NaiveBayes -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.RandomTree -depth 3

Average mutual information between the nominal attributes and the target attribute.

Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.REPTree -L 1

Error rate achieved by the landmarker weka.classifiers.bayes.NaiveBayes -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W

Error rate achieved by the landmarker weka.classifiers.trees.RandomTree -depth 3