Progress Report, Friday, January 12th , 2018, 1400, CB3

Bradley Joseph Nartowt

January 12, 2018

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 1/5
Goals for Friday, January 12, 2018

Read papers and take notes on them.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)
Resolve low PPV value.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)
Resolve low PPV value. (ONGOING)

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)
Resolve low PPV value. (ONGOING)
Write introduction

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)
Resolve low PPV value. (ONGOING)
Write introduction (OUTLINE TO BE PRESENTED)

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)
Resolve low PPV value. (ONGOING)
Write introduction (OUTLINE TO BE PRESENTED)
Wish-list of figures

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Goals for Friday, January 12, 2018

Read papers and take notes on them. Notes to later become

papers/F-32 proposal. (ONGOING)
Resolve low PPV value. (ONGOING)
Write introduction (OUTLINE TO BE PRESENTED)
Wish-list of figures (TO BE PRESENTED)

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 2/5
Manuscript outline - introduction

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1]

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7]

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7] → not highest accuracy,
but most widely and cheaply implementable in real-time (to, e.g., send
text-message [8] reminders)

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7] → not highest accuracy,
but most widely and cheaply implementable in real-time (to, e.g., send
text-message [8] reminders)
2 causes of colorectal cancer not gauranteed to be in dataset

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7] → not highest accuracy,
but most widely and cheaply implementable in real-time (to, e.g., send
text-message [8] reminders)
2 causes of colorectal cancer not gauranteed to be in dataset → design
future surveys accordingly

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7] → not highest accuracy,
but most widely and cheaply implementable in real-time (to, e.g., send
text-message [8] reminders)
2 causes of colorectal cancer not gauranteed to be in dataset → design
future surveys accordingly
4 Limits: survey questions are asked of general public.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7] → not highest accuracy,
but most widely and cheaply implementable in real-time (to, e.g., send
text-message [8] reminders)
2 causes of colorectal cancer not gauranteed to be in dataset → design
future surveys accordingly
4 Limits: survey questions are asked of general public. May ask:
1 “Smoking habits?”

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Manuscript outline - introduction

1 very brief description of what colorectal cancer is [1] early detection =

means of reducing mortality
2 very brief summary of studies of causes e.g., alcohol in early tumor
development [2], colorectal cancer in Alaskan natives [3] [4],
3 brief summary of/advantages+disadvantages methods of detecting
colorrectal cancer
1 among which is machine-learning [5] [6] [7] → not highest accuracy,
but most widely and cheaply implementable in real-time (to, e.g., send
text-message [8] reminders)
2 causes of colorectal cancer not gauranteed to be in dataset → design
future surveys accordingly
4 Limits: survey questions are asked of general public. May ask:
1 “Smoking habits?” • perhaps not “colorectal inflammation?”

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 3/5
Proposed figures and tabales

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 4/5
Proposed figures and tabales

1 Make 13 × 13 table for 13 features in data-set.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 4/5
Proposed figures and tabales

1 Make 13 × 13 table for 13 features in data-set. → fit function

y (xi , xj ) = ci xi + cj xj and report ci in (i, j)th entry and cj in (j, i)th of
table, ± confidence-interval, ri .

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 4/5
Proposed figures and tabales

1 Make 13 × 13 table for 13 features in data-set. → fit function

y (xi , xj ) = ci xi + cj xj and report ci in (i, j)th entry and cj in (j, i)th of
table, ± confidence-interval, ri . If ci & ri , color-code as red →
qualitative significance of factor.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 4/5
Proposed figures and tabales

1 Make 13 × 13 table for 13 features in data-set. → fit function

y (xi , xj ) = ci xi + cj xj and report ci in (i, j)th entry and cj in (j, i)th of
table, ± confidence-interval, ri . If ci & ri , color-code as red →
qualitative significance of factor.
2 AUC with error-bars for factors determined to be qualitatively
significant by above Table. Use double-y axes.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 4/5
Proposed figures and tabales

1 Make 13 × 13 table for 13 features in data-set. → fit function

y (xi , xj ) = ci xi + cj xj and report ci in (i, j)th entry and cj in (j, i)th of
table, ± confidence-interval, ri . If ci & ri , color-code as red →
qualitative significance of factor.
2 AUC with error-bars for factors determined to be qualitatively
significant by above Table. Use double-y axes.
3 Quantity of interest Sensitivity/specificity/PPV vs. cutoff value.
(Pick better cutoff by eyeballing...). Indicate units.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 4/5
PROBLEM: PPV ∼ 10−2 as a result of using m[50,64] ≈ 90, f[50,64] ≈ 65
m≥65 ≈ 275, f≥65 ≈ 215.

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 5/5
PROBLEM: PPV ∼ 10−2 as a result of using m[50,64] ≈ 90, f[50,64] ≈ 65
m≥65 ≈ 275, f≥65 ≈ 215.
Figure 5. Trends in Colorectal Cancer Incidence (1975-2013) and Mortality (1970-2014) Rates by Age and Sex, US
Incidence Mortality
Ages 20-49 5
Ages 20-49
15

12 4

Rate per 100,000 population

Rate per 100,000 population
Male
Male
9 3

Female Female
6 2

3 1

0 0
1975 1980 1985 1990 1995 2000 2005 2010 1970 1975 1980 1985 1990 1995 2000 2005 2010

Ages 50-64 50
Ages 50-64
140

120
Male 40 Male

Rate per 100,000 population

Rate per 100,000 population

100

30
80

60 Female 20 Female

40
10
20

0 0
1975 1980 1985 1990 1995 2000 2005 2010 1970 1975 1980 1985 1990 1995 2000 2005 2010

Ages 65+ Ages 65+

500 250

Male
400 200 Male

Rate per 100,000 population

Rate per 100,000 population

300 150

Female
Female
200 100

100 50

0 0
1975 1980 1985 1990 1995 2000 2005 2010 1970 1975 1980 1985 1990 1995 2000 2005 2010

R
 ates are age adjusted to the 2000 US standard population and are adjusted for reporting delays.
Source: I ncidence – SEER Program, National Cancer Instititue, 2016. Mortality – National Center for Health Statistics, Centers for Disease Control and Prevention, 2016.
©2017 American Cancer Society, Inc., Surveillance Research
Figure: Prevalence, PD , is able to be estimated from data from the American
improvements in treatment (12%), changing patterns in both men and women, compared to declines of about 2%
Cancer Society [9] data on colorectal cancer-incidence (left) and mortality (right).
CRC risk factors (35%), and screening (53%).31 The rate of per year during the 1990s. However, progress has lagged
decline accelerated slightly in the past decade; from 2005 in the highest-poverty areas of the US, including the
Bradley Joseph to
Nartowt 2014, rates decreased by an average of 2.5% per year
Progress, 2018-01-12, in lower Mississippi
1400, Delta
CB3 and parts of Appalachia.34 January 12, 2018 5/5
A. C. S. (press release), “What is colorectal cancer?,”
V. G. A. B. E. B. C. H. F. C. J.-C. C. S. N. M Bardou,
S Montembault, “Excessive alcohol consumption favours high risk
polyp or colorectal cancer occurrence among patients with adenomas:
a case control study,” vol. 50, p. 38.
F. S. A. P. L. Janet J. Kelly, Steven R. Alberts, “Colorectal cancer in
alaska native people (2005 to 2009),”
Y. R. A. D. News), “New test targets alaska natives’ high rate of
colorectal cancer,”
J. A. Cruz and D. S. Wishart, “Applications of machine learning in
cancer prediction and prognosis (review),”
K. P. E. M. V. K. D. I. F. Konstantina Kourou, Themis P. Exarchos,
“Machine learning applications in cancer prognosis and prediction,”
A. B. Jean-Emmanuel Bibault, Philippe Giraud, “Big data and
machine learning in radiation oncology: State of the art and future
prospects,”
Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 5/5
P. M. . J. J. S. M. . M. A. J. M. . V. H. P. . D. A. D. P. . Clemma
J. Muller, PhD ; Renee F. Robinson and M. Dedra Buchwald, “Text
message reminders increased colorectal cancer screening in a
randomized trial with alaska native and american indian people,”
vol. 123, p. 1382.
M. A. J. D. P. Rebecca Siegel, MPH; Kimberly Miller, “Colorectal
cancer facts and figures 2017 to 2019,”

Bradley Joseph Nartowt Progress, 2018-01-12, 1400, CB3 January 12, 2018 5/5