Challenges for the Computational

Discovery of Scientific Knowledge

Pat Langley
School of Computing and Informatics
Arizona State University
Tempe, Arizona
Institute for the Study of Learning and Expertise
Palo Alto, California

Thanks to K. Arrigo, D. Billman, M. Bravo, S. Borrett, W. Bridewell, S. Dzeroski, and

L. Todorovski for their contributions to this research, which is funded by a grant from
the National Science Foundation.
 Drawbacks of Scientific Data Mining

Because it borrows from work on commercial applications, most

work on scientific data mining:

• generates models in forms inappropriate to most sciences

• makes incorrect assumptions about the available inputs
• focuses on convenient algorithmic issues, not scientists’ needs

We need to redirect attention toward a broader range of discovery

tasks that actually arise in scientific fields.
Data-mining researchers would benefit from looking at the older
literature on computational scientific discovery.
 Claim 1: Scientific Notations
Traditional data-mining notations are not easily understood by or
communicated to domain scientists.
Most sciences state and communicate models in formalisms they
have used for decades.
We need more work on discovering scientific knowledge cast in
communicable forms (Dzeroski & Todorovski, 2007).

Ecosystem model Gene regulation model

NPPc = Σmonth max (E · IPAR, 0)
E = 0.56 · T1 · T2 · W
NBLR NBLA PBS
T1 = 0.8 + 0.02 · Topt – 0.0005 · Topt2 + + -
T2 = 1.18 / [(1 + e 0.2 · (Topt – Tempc – 10) ) · (1 + e 0.3 · (Tempc – Topt – 10) )] -
W = 0.5 + 0.5 · EET / PET DFR psbA1 Health
+
PET = 1.6 · (10 · Tempc / AHI)A · PET-TW-M if Tempc > 0 - -
PET = 0 if Tempc < 0 + -
+ RR psbA2 Photo
A = 0.00000068 · AHI3 – 0.000077 · AHI2 + 0.018 · AHI + 0.49 +
IPAR = 0.5 · FPAR-FAS · Monthly-Solar · Sol-Conver -
FPAR-FAS = min [(SR-FAS – 1.08) / SR (UMD-VEG) , 0.95] Light cpcB
SR-FAS = (Mon-FAS-NDVI + 1000) / (Mon-FAS-NDVI – 1000)
 Claim 2: Background Knowledge
Scientists often have initial knowledge that should influence the
discovery process.
Ignoring this knowledge can produce models that scientists reject
as nonsensical (Pazzani et al., 2001).

Observations

NBLR NBLA PBS

+ + -
+

Model DFR
-
psbA1
+
Health
-
Revision -
+
RR
× psbA2
× Photo

-
NBLR NBLA PBS Light cpcB
+ + -
-
DFR psbA1 Health
-
+ Revised model
-
+ -
RR psbA2 Photo
+ +
Light
-
cpcB Initial model
 Claim 3: Small Data Sets
Most data-mining work assumes that large data sets are available.
But in many scientific domains, data are rare and hard to obtain.
Discovering scientific knowledge from small data sets raises an
entirely different set of challenges (Lee et al., 1998).
We need more research on this important aspect of discovery.

Ecosystem model Gene regulation model

Number of variables 8 Number of variables 9

Number of equations 11 Number of initial links 11
Number of parameters 20 Number of possible links 70
Number of samples 303 Number of samples 20
 Claim 4: Scientific Explanation
Most work on data mining finds models that, although accurate,
merely describe the observations.
However, scientists often want models that explain their data using
familiar concepts.
Explanatory models can include theoretical entities and processes
that link back to domain knowledge (Langley et al., 2002).

Ecosystem model Gene regulation model

NPPc

NBLR NBLA PBS

+ + -
E IPAR -
DFR psbA1 Health
+
e_max W T2 T1 SOLAR FPAR - -
+ -
+ RR psbA2 Photo
A PET EET Topt SR +
-
Light cpcB
AHI PETTWM Tempc NDVI VEG
 Claim 5: Interactive Discovery
Most data-mining work focused on entirely automated algorithms.
But most scientists want computational aids rather than systems that
would replace them.
We need more work on interactive discovery (Bridewell et al., 2007).

Domain user

NBLR NBLA PBS

+ + -
+

Model DFR
-
psbA1
+
Health
-
Observations Revision -
+
RR
× psbA2
× Photo

-
NBLR NBLA PBS Light cpcB
+ + -
-
DFR psbA1 Health
-
+ Revised model
-
+ -
RR psbA2 Photo
+ +
Light
-
cpcB
Initial model
The PROMETHEUS System
(Bridewell et al., 2007)