20150930 New York Academy of Sciences

1. brian m. bot | principal scientist |
the beginnings of an open ecosystem
in
2015 sep 30
sage bionetworks
mHealth
the new york academy of sciences

2. mHealth

4. move beyond insular health tracking

6. >75%

8. how to balance desire to share w/
importance of privacy?

9. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
our approach

10. a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
sage bionetworks
our approach

11. Wisdom'of'the'crowd'
Ci0zen'engagement'
Data'sharing'
Open'
Collabora0ve'
Research'
Gamifica0on'
Community'Development'
Consor0a'/'Federa0on'
sage bionetworks

13. the beginnings of an open ecosystem in mHealth

16. moving beyond the app
participant
centered
consent

17. open source toolkit
participant-centered consent
http://sagebase.org/pcc

18. 1. tiered information access by
participants
2. ‘pictorial’ dominant on first information
tier
3. text dominant on second information
tier
4. require perfect score on short
assessment
participant-centered consent

22. radical honesty > radical restrictions

23. changeable by participant

24. > 70% choose to “share broadly”
~75k participants across all studies

25. balance the security settings of
the system with the desires of
those being studied

27. security as ‘prevent access as
much as possible’ isn’t the
answer

28. give researchers the tools to do
the right thing

29. open RESTful APIs
www.synapse.org
programmatic clients

30. access rights for controlled sharing
analyses tracked with versioning and provenance
publication and sharing for reproducibility
a research commons enabling secondary research

31. access rights for controlled sharing

32. access rights for controlled sharing

33. code in github
data in synapse
results in synapse
analyses tracked with versioning and provenance

34. publication and sharing for reproducibility

35. publication and sharing for reproducibility

36. promote an ecosystem where
for others to consume
is conductedresearch

37. research

38. 38
mPower

39. 39
• 59,700 downloads from app store
• 16,585 participants consented (28% of total downloaded)
• 15,185 participants enrolled (92% of all consented)
• 78% of participants chose to share data broadly
• 17% of participants who completed enrollment survey indicate
a diagnosis of Parkinson disease (1501/8715)
mPower

40. Passive
Measures
GPS -
Displacement
Vectors
GPS -
Displacement
Vectors
- -
Structured
Activities
Tapping
Activity
Walking/
Standing
Activity
Voice Activity
Memory
Game
Surveys
MDS-UPDRS
PDQ8
MDS-UPDRS
PDQ8
MDS-UPDRS
PDQ8
MDS-UPDRS
PDQ8
four symptoms of PD
Motor
Initiation
Gait/Balance Hypophonia Memory

41. Motor
Initiation
Gait/Balance Hypophonia Memory

42. Standard
Structured Activities
Passive Measures
• High Friction (long, infrequent)
• Validated in large cohorts
• Basis for most publications
• Mild Friction (more frequent)
• Minimal validation
• Minimal Friction
• Not validated
mPower

43. 43
Traditional Measures First-order Features
Number of Taps
Number of taps, Mean tapping interval, Median tapping interval,
Minimum tapping interval, maximum tapping interval, Standard
deviation of tapping interval, Kurtosis of tapping interval,
Interquartile range of tapping interval, Interquartile range of right
button X, Range right button X ,Standard deviation right button X,
Interquartile range of left button X, Range left button X ,Standard
deviation left button X, Interquartile range of right button Y, Range
right button Y ,Standard deviatiion right button Y, Interquartile
range of left button Y, Range left button Y ,Standard deviation left
button Y, Correlation X and Y, Skew tapping interval, No-button
tapping frequency, Fatigue at 10%, Fatigue at 25%, Fatigue at
50%, Mean drift left, Mean drift right, min Drift left, min Drift right,
Max drift left, Max drift right, IQR drift left, IQR drift right, skew drift
left, Skew drift right, Kurtosis drift left, Kurtosis drift right, Range
drift left, Range drift right, CV drift left, CV drift right
traditional vs. digital measures

44. 62 year old man
2009 onset of symptoms
2009 start meds
mean change: 51 taps
max change: 111 taps
min change: -21 taps
67 year old woman
2004 onset of symptoms
2009 start meds
mean change: -4 taps
max change: 28 taps
min change: -38 taps

45. ●
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original shuffled
0.30.40.50.60.70.80.91.0
before/after medication classif.
balancedaccuracy
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kurTappingInter
buttonNoneFreq
medianTappingInter
minTappingInter
maxTappingInter
skewTappingInter
rangeLeftY
madTappingInter
meanTappingInter
rangeLeftX
sdLeftX
iqrTappingInter
numberTaps
sdRightX
iqrLeftY
sdLeftY
iqrRightX
rangeRightX
iqrLeftX
sdTappingInter
iqrRightY
corXY
rangeRightY
sdRightY
0
1
2
3
4
tapping features only
Importance
54d6
before
after
other
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6080100
6899ba07−f868−49db−9651−3504b6d754d6
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corXY
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iqrLeftY
rangeLeftX
sdLeftX
skewTappingInter
iqrLeftX
sdLeftY
buttonNoneFreq
iqrRightY
sdRightY
rangeRightX
corXY
rangeRightY
sdRightX
rangeLeftY
iqrRightX
madTappingInter
iqrTappingInter
kurTappingInter
sdTappingInter
maxTappingInter
minTappingInter
medianTappingInter
meanTappingInter
numberTaps
0
2
4
6
8
tapping features only
Importance
ore
r
er
●
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0.30.40.5
bda58cbf−a773−487d−bbc4−2fe367e0fcc2
edianTappingInter
before
after
other
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62 year old man
Number of Taps
Mean Tapping Interval
Median Tapping Interval
67 year old woman
Standard Deviation R Y
Range Right Y
Correlation X Y
same medicine, different impacts

46. don't
other
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
16 − original − numberTaps − 8beab5c6−6067−4c47−b655−1901f5a534a8
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
be
25 − original − numberTaps − 487959bf−bab4−488a−a9ae−67b4e645f347
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
be
30 − original − numberTaps − 5c525b29−bf01−47ea−ba44−4261a8325b7b
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
be
31 − original − numberTaps − 8ef4e9c3−c701−47e4−bec5−4ca64dbdadc7
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
be
54 − original − numberTaps − 61e223ac−4657−48b8−89b0−d37df5c85d39
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
be
66 − original − numberTaps − ac7c3961−9268−42b7−aeb7−fc4c49c7a6bb
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
d
o
be
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Apr May Jun Jul Aug Sep
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numberTaps
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Apr May Jun Jul Aug Sep
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Apr May Jun Jul Aug Sep
160180200220240
63 − 43294479−32e0−4589−92ee−269b36a70e46
numberTaps
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Apr May Jun Jul Aug Sep
6080100120140160180
64 − 72f75a4d−de63−4077−b77e−49d98f559e8c
numberTaps
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Apr May Jun Jul Aug Sep
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Apr May Jun Jul Aug Sep
406080100120140160
66 − ac7c3961−9268−42b7−aeb7−fc4c49c7a6bb
numberTaps
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67 − b2a760b7−bd2d−4918−a7b7−6fa385423e11
numberTaps
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numberTaps
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don't
other
after
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
don't
other
after
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
23 − original − audio.Median_F0 − 9884c3bf−86bb−4370−acbf−19db34cf297c
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
23 − detrended − audio.Median_F0 − 9884c3bf−86bb−4370−acbf−19db34cf297c
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
24 − original − audio.Median_F0 − 1ff805eb−4e96−4d64−b7a4−cc54aaddf2d6
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
24 − detrended − audio.Median_F0 − 1ff805eb−4e96−4d64−b7a4−cc54aaddf2d6
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
25 − original − audio.Median_F0 − 7457113a−34bd−4324−935c−f66bd33f1e4b
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
25 − detrended − audio.Median_F0 − 7457113a−34bd−4324−935c−f66bd33f1e4b
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
26 − original − audio.Median_F0 − ac7c3961−9268−42b7−aeb7−fc4c49c7a6bb
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
26 − detrended − audio.Median_F0 − ac7c3961−9268−42b7−aeb7−fc4c49c7a6bb
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
27 − original − audio.Median_F0 − 65883b0e−ec25−4883−9019−ae20a495b072
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
27 − detrended − audio.Median_F0 − 65883b0e−ec25−4883−9019−ae20a495b072
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
28 − original − audio.Median_F0 − a50dfd03−6211−47ff−9d94−8026c65eed93
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
28 − detrended − audio.Median_F0 − a50dfd03−6211−47ff−9d94−8026c65eed93
don't
other
after
before
Mar 9 Apr 1 May 1 Jun 1 Jul 1 Aug 1 Sep 1
29 − original − audio.Median_F0 − f8d44faa−f71a−43be−9fa8−8d381b9cc380
other
after
before
29 − detrended − audio.Median_F0 − f8d44faa−f71a−43be−9fa8−8d381b9cc380
other
after
before
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Apr May Jun Jul Aug Sep
6080100120140160180
23 − audio.Median_F0 − 9884c3bf−86bb−4370−acbf−19db34cf297c
audio.Median_F0
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24 − audio.Median_F0 − 1ff805eb−4e96−4d64−b7a4−cc54aaddf2d6
audio.Median_F0
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Apr May Jun Jul Aug Sep
120140160180200
25 − audio.Median_F0 − 7457113a−34bd−4324−935c−f66bd33f1e4b
audio.Median_F0
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160180200220240260
26 − audio.Median_F0 − ac7c3961−9268−42b7−aeb7−fc4c49c7a6bb
audio.Median_F0
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180200220240
27 − audio.Median_F0 − 65883b0e−ec25−4883−9019−ae20a495b072
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Apr May Jun Jul Aug Sep
100150200250
28 − audio.Median_F0 − a50dfd03−6211−47ff−9d94−8026c65eed93
audio.Median_F0
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Apr May Jun Jul Aug Sep
100120140160180200
29 − audio.Median_F0 − f8d44faa−f71a−43be−9fa8−8d381b9cc380
audio.Median_F0
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105110115120125
30 − audio.Median_F0 − 9cf05509−f169−4b4b−8ef5−3124213f3d8e
audio.Median_F0
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scorecard of sensor-based phenotypes
for clinical tracking
tappingvoice
shuffled
fter medication classif.
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iqrLeftY
rangeLeftX
sdLeftX
skewTappingInter
iqrLeftX
sdLeftY
buttonNoneFreq
iqrRightY
sdRightY
rangeRightX
corXY
rangeRightY
sdRightX
rangeLeftY
iqrRightX
madTappingInter
iqrTappingInter
kurTappingInter
sdTappingInter
maxTappingInter
minTappingInter
medianTappingInter
meanTappingInter
numberTaps 0
2
4
6
8
tapping features only
Importance
3−487d−bbc4−2fe367e0fcc2
before
after
other
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0.30.40.5
bda58cbf−a773−487d−bbc4−2fe367e0fcc2
appingInter
before
after
other
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47. impact care by empowering a dialogue
between patient and physician

48. brian m. bot
————————
principal scientist
community manager
sage bionetworks
brian.bot@sagebase.org
@BrianMBot
thank you