LIFE SCIENCE DATA MINING (Science, Engineering, and Biology Informatics) by Stephen Tin Chi Wong, PDF, EPUB, 981270065X

LIFE SCIENCE DATA MINING (Science, Engineering, and Biology Informatics) by Stephen Tin Chi Wong

  • Print Length: 388 Pages
  • Publisher: World Scientific Publishing
  • Publication Date: December 29, 2006
  • Language: English
  • ISBN-10: 981270065X, 9812700641
  • ISBN-13: 978-9812700650, 978-9812700643
  • File Format: PDF, EPUB

 

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PREFACE
Data mining is the process of using computational algorithms and tools
to automatically discover useful information in large data archives. Data
mining techniques are deployed to score large databases in order to find
novel and useful patterns that might otherwise remain unknown. They
also can be used to predict the outcome of a future observation or to
assess the potential risk in a disease situation. Recent advances in data
generation devices, data acquisition, and storage technology in the life
sciences have enabled biomedical research and healthcare organizations
to accumulate vast amounts of heterogeneous data that is key to
important new discoveries or therapeutic interventions. Extracting useful
information has proven extremely challenging however. Traditional data
analysis and mining tools and techniques often cannot be used because of
the massive size of a data set and the non-traditional nature of the
biomedical data, compared to those encountered in financial and
commercial sectors. In many situations, the questions that need to be
answered cannot be addressed using existing data analysis and mining
techniques, and thus, new algorithms and methods need to be developed.
Life science is an important application domain that requires new
techniques of data analysis and mining. This is one of the first technical
books focusing on the data analysis and mining techniques in life science
applications. In this introductory chapter, we present the key topics to be
covered in this book. In Chapter 1 “Taxonomy of early detection for
environmental and public health applications,” Chung-Sheng Li of IBM
Research provides a survey of early warning systems and detection
approaches in terms of problem domains and data sources. The chapter
introduces current syndromic surveillance prototypes or deployments and
defines the problem domain for three classes: individual and public
health level, cellular level, and molecular level. For data sources, they
were also categorized into three parts including clinically related data,
non-traditional data, and auxiliary data. Furthermore, data sources can be
characterized by three dimensions (structured, semi-structured, and non-
structured).
VI
Preface
In Chapter 2 “Time-lapse cell cycle quantitative data analysis using
Gaussian mixture models,” Xiaobo Zhou and colleagues at Harvard
Medical School describe an interesting and important emerging
technology area of high throughput biological imaging. The authors
address the unresolved problem of identifying the cell cycle process
under different conditions of perturbation. In the study, the time-lapse
fluorescence microscopy imaging images are analyzed to detect and
measure the duration of various cell phases, e.g., inter phase, prophase,
metaphase, and anaphase, quantitatively.
Chapter 3 “Diversity and accuracy of data mining ensemble” by
Wenjia Wang of the University of East Anglia discusses an important
issue: classifier fusion or an ensemble of classifiers. This paper first
describes why diversity is essential and how the diversity can be
measured, then it analyses the relationships between the accuracy of an
ensemble and the diversity among its member classifiers. An example is
given to show that the mixed ensembles are able to improve the
performance.
Various clustering algorithms have been applied to gene expression
data analysis. Chapter 4 “Integrated clustering for microarray data” by
Gabriela Moise and Jorg Sander from the University of Alberta argue
that the integration strategy is a “majority voting” approach based on the
assumption that objects belong to a “natural” cluster are likely to be co-
located in the same cluster by different clustering algorithms. The
chapter also provides an excellent survey of clustering and integrated
clustering approaches in microarray analysis.
EEG has a variety of applications in basic and clinic neuroscience.
Chapter 5: “Complexity and Synchronization of EEG with Parametric
Modeling” by Xiaoli Li presents a nice work on parametric modeling
of the complexity and synchronization of EEG signals to assist the
diagnosis of epilepsy or the analysis of EEG dynamics.
In Chapter 6: “Bayesian Fusion of Syndromic Surveillance with
Sensor Data for Disease Outbreak Classification,” by Jeffrey Lin,
Howard Burkom, et al. from The Johns Hopkins University Applied
Physics Laboratory and Walter Reed Army Institute for Research
describe a novel Bayesian approach to fuse sensor data with syndromic
surveillance data presented for timely detection and classification of
Preface
vn
disease outbreaks. In addition, the authors select a natural disease,
asthma, which is highly dependent on environmental factors to validate
the approach.
Continuing the theme of syndromic surveillance, in Chapter 7: “An
Evaluation of Over-the-Counter Medication Sales for Syndromic
Surveillance,” Murray Campbell, Chung Sheng Li, et al. from IBM
Watson Research Center describe a number of approaches to evaluate the
utility of data sources in a syndromic surveillance context and show that
there may be some values in using sales of over-the-counter medications
for syndromic surveillance.
In Chapter 8: “Collaborative Health Sentinel” JH Kaufman, G Decad,
et al. from IBM Research Divisions in California, New York, and Israel
provide a clear survey and highlight the approach of significant trends,
issues and further directions for global systems for health management.
They addressed various issues for systems covering general environment
and public health, as well as global view.
In Chapter 9: “Data Mining for Drug Abuse Research and Treatment
Evaluation: Data Systems Needs and Challenges” Mary Lynn Brecht of
UCLA argues that drug abuse research and evaluation can benefit from
data mining strategies to generate models of complex dynamic
phenomena from heterogeneous data sources. She presents a user’s
perspective and several challenges on selected topics relating to the
development of an online processing framework for data retrieval and
mining to meet the needs in this field.
The increasing amount and complexity of data used in predictive
toxicology call for new and flexible approaches based on hybrid
intelligent methods to mine the data. To fill this needs, in Chapter 10
“Knowledge Representation for Versatile Hybrid Intelligent Processing
Applied in Predictive Toxicology”, Daneil Neagu from Bradford
University, England addresses the issue of devising a mark-up language,
as an application of XML (Extensible Markup Language), for
representing knowledge modeling in predictive toxicology – PToXML
and the markup language HISML for integrated data structures of Hybrid
Intelligent Systems.
Ensemble classification is an active field of research in pattern
recognition. In Chapter 11: “Ensemble Classification System
Vlll
Preface
Implementation for Biomedical Microarray Data,” Shun Bian and
Wenjia Wang of the University of East Anglia, UK present a framework
of developing a flexible software platform for building an ensemble
based on the diversity measures. An ensemble classification system
(ECS) has been implemented for mining biomedical data as well as
general data.
Time-lapse fluorescence microscopy imaging provides an important
high throughput method to study the dynamic cell cycle process under
different conditions of perturbation. The bottleneck, however, lies in the
analysis and modeling of large amounts of image data generated.
Chapter 12: “An Automated Method for Cell Phase Identification in
High Throughput Time-Lapse Screens” by Xiaowei Chen and colleagues
from Harvard Medical School describe the application of statistical and
machine learning techniques to the problem of tracking and identifying
the phase of individual cells in populations as a function of time using
high throughput imaging techniques.
Modeling gene regulatory networks has been an active area of
research in computational biology and systems biology. An important
step in constructing these networks involves finding genes that have the
strongest influence on the target gene. In Chapter 13, “Inference of
Transcriptional Regulatory Networks based on Cancer Microarray
Data,” Xiaobo Zhou and Stephen Wong from Harvard Center for
Neurodegeneration and Repair address this problem. They start with
certain existing subnetworks and methods of transcriptional regulatory
network construction and then present their new approach.
In Chapter 14: “Data Mining in Biomedicine,” Lucila Ohno-Machado
and Staal Vinterbo of Brigham and Women’s Hospital provide an
overview of data mining techniques in biomedicine. They refer to data
mining as any data processing algorithm that aims to determine patterns
or regularities in the data. The patterns may be used for diagnostic or
prognostic purposes and the models that result from pattern recognition
algorithms will be refereed to as predictive models, regardless of whether
they are used to classify. The chapter provides readers an excellent
introduction about data mining and its applications to the readers.
Association rules mining is a popular technique for the analysis of
gene expression profiles like microarray data. In Chapter 15: “Mining
Preface IX
Multilevel Association Rules from Gene Ontology and Microarray
Data,” VS Tseng and SC Yang from National Cheng Kung University,
Taiwan, aim at combining microarray data and existing biological
network to produce multilevel association rules. They propose a new
algorithm for mining gene expression transactions based on existing
algorithm ML_T1LA in the context of Gene Ontology and a filter
version CMAGO.
Optical biosensors are now utilized in a wide range of applications,
from biological-warfare-agent detection to improving clinical diagnosis.
In Chapter 16, “A Proposed Sensor-Configuration and Sensitivity
Analysis of Parameters with Applications to Biosensors,” HJ Halim from
Liverpool JM University, England, introduces a configuration of sensor
system and analytical model equations to mitigate the effects of internal
and external parameter fluctuations.
The subject of data mining in life science, while relatively young
compared to data mining in other application fields, such as finance and
marketing, or to statistics or machine learning, is already too large
to cover in a single book volume. We hope that this edition would
provide the readers some of the specific challenges that motivate the
development of new data mining techniques and tools in life sciences
and serve as an introductory material to the researchers and practitioners
interested in this exciting field of application.
Stephen TC Wong and Chung-Sheng Li

CHAPTER 1
SURVEY OF EARLY WARNING SYSTEMS FOR
ENVIRONMENTAL AND PUBLIC HEALTH APPLICATIONS
Chung-Sheng Li
IBM T. J. Watson Research Center, PO Box 704, Yorktown Heights, NY 10598
1. Introduction
Advances in sensors and actuators technologies and real-time analytics
recently have accelerated the adoption of real-time or near real-time
monitoring and alert generation for environmental and public health
related activities.
Monitoring of environmental related activities include the use of
remote sensing (satellite imaging and aerial photo) for tracking the
impacts due to global climate change (e.g. detection of thinning polar ice
as evidence of global warming, deforestation in the Amazon region),
tracking the impact of natural and man-made disasters (e.g. earthquakes,
tsunami, volcano eruptions, floods, and hurricane), forest fire, and
pollution (including pollution of air, land, and water).
Early warnings for human disease or disorder at the individual
level often rely on various symptoms or biomarkers. For example,
retina scan has been developed as a tool for early diagnosis of
diabetic retinopathy [Denninghoff 2000]. CA 125, a protein found in
blood, has been used as the biomarker for screening early stages of
ovarian cancer. The level of Prostate Specific Antigen (PSA) has
been used for early detection of prostate cancer (usually in conjunction
with a digital rectal exam). National Cancer Institute of NTH has
sponsored the forming of the Early Detection Research Network (EDRN
1
2 C.-S. Li
http://www3.cancer.gov/prevention/cbrg/edrn/) program since 1999.
This comprehensive effort includes the development and validation of
various biomarkers for detecting colon, liver, kidney, prostate, bladder,
breast, ovary, lung, and pancreatic cancer.
Health and infectious disease surveillance for public health purposes
have existed for many decades. Currently, World Health Organization
(WHO) has set up a Global Outbreak Alert & Response Network
(GOARN) to provide surveillance and response for communicable
diseases around the world (http://www.who.int/csr/outbreaknetwork/en/).
Examples of the diseases tracked by GOARN include anthrax, influenza,
Ebola hemorrhagic fever, plague, smallpox, and SARS. The alert and
response operations provided include epidemic intelligence, event
verification, information management and dissemination, real time alert,
coordinated rapid outbreak response, and outbreak response logistics.
For the United States, the National Center for Infectious Diseases
(NCID) at CDC has set up 30+ surveillance networks (see Section 2) to
track individual infectious diseases or infectious disease groups.
Monitoring disease outbreaks for public health purposes based on
environmental epidemiology has been demonstrated for a number of
vector-born infectious diseases such as Hantavirus Pulmonary Syndrome
(HPS), malaria, Lyme disease, West Nile virus (WNV), and Dengue
fever [Glass 2001a, Glass 2001b, Glass 2002, Klein 2001a, Klein
2001b]. In these cases, environmental effects such as the change of
ground moisture, ground temperature, and vegetation due to El Nino and
other climate changes facilitate the population change of disease hosts
(such as mosquitoes and rodents). These changes can then cause
increased risk of diseases in the human population.
Recently, a new trend to track subtle human behavior changes due to
disease outbreak has emerged to provide advanced warnings before
significant casualties registered from clinical sources. This approach is
also referred to in the literature as syndromic surveillance (or early
detection of disease outbreaks, pre-diagnosis surveillance, non-traditional
surveillance, enhanced surveillance, non-traditional surveillance, and
disease early warning systems). This approach has received substantial
interests and enthusiasm during the past few years, especially after Sept.
Survey of Early Warning Systems 3
11, 2001 [Buehler 2003, Duchin 2003, Goodwin2004, Mostashari 2003,
Pavlin 2003, Sosin 2003, and Wagner 2001].
In this chapter, we surveyed the most widely adopted disease
surveillance techniques, early warning systems, and detection approaches
in terms of problem domain and data sources. This survey intends to
facilitate the clarification and discovery of interdependency among
problem domains, data sources, and detection methods and thus facilitate
sharing of data sources and detection methods across multiple problem
domains, when appropriate.
2. Disease Surveillance
Health and infectious disease surveillance for public health purposes
have existed for many decades. The following is a subset of the 30+
national surveillance systems coordinated by the National Center of
Infectious Disease (NCID) at CDC (http://www.cdc.gov/ncidod/osr/site/
surv_resources/surv_sy s .htm).
Mortality Reporting System: from 122 cities & metropolitan areas,
compiled by the CDC epidemiology program office;
Active Bacterial Core Surveillance (ABCs): at ten emerging infectious
program sites such as California, Colorado, Connecticut, Georgia, etc.;
BaCon Study: on assessing the frequency of blood component bacterial
contamination associated with transfusion;
Border Infectious Disease Surveillance Project (BIDS): focusing on
hepatitis and febrile-rash illness along the US-Mexico border;
Dialysis Surveillance Network (DSN): focus on tracking vascular
access infections and other bacterial infections in hemodialysis patients;
Electronic Foodborne Outbreak Investigation and Reporting System
(EFORS): used by 50 states to report data about Foodborne Outbreaks
on a daily basis;
EMERGEncy ID NET: focus on emerging infectious disease based on
11 university affiliated urban hospital emergency departments;
Foodborne Diseases Active Surveillance Network (FoodNet): consists
of active surveillance for foodborne diseases and related epidemiologic
studies. This is a collaboration among CDC, the ten emerging infectious
program sites (EIPs), the USD A, and FDA;
4 C.-S. Li
Global Emerging Infectious Sentinel Network (GeoSentinel): consists
of travel/tropical medicine clinics around the world that monitor
geographic and temporal trends in mobility;
National Notifiable Diseases Surveillance System (NNDSS): The
Epidemiology Program Office (EPO) at CDC collect, compile, and
publish reports of disease considered as notifiable at the national level;
National West Nile Virus Surveillance System: Since 2000, 48 states
and 4 cities started to collect data about wild birds, sentinel chicken
flocks, human cases, veterinary cases, and mosquito surveillance;
Public Health Laboratory Information System (PHLIS): Collects
data on cases/isolates of specific notifiable diseases from every state
within the United States.
United States Influenza Sentinel Physicians Surveillance Network:
250+ physicians around the country report each week the number of
patients seen and the total number with flu-like symptoms;
Waterborne-Disease Outbreak Surveillance System: includes data
regarding outbreaks associated with drinking water and recreational
water.
The US DoD Global Emerging Infectious Surveillance System (DoD-
GEIS): has its own set of surveillance network within the States as well
as internationally (http://www.geis.fhp.osd.mil/).
A number of syndromic surveillance prototypes or deployments have
been developed recently:
BioSense: a national initiative at US (coordinated by CDC) to establish
near real-time electronic transmission of data to local, state, and federal
public health agencies from national, regional, and local health data by
accessing and analyzing diagnostic and prediagnostic health data.
RODS (Real Time Outbreak and Disease Surveillance
http://rods.health.pitt.edu/): a joint effort between University of
Pittsburgh and CMU. This effort includes an open source version of
RODS software (since 2003) and National Retail Data Monitor (NRDM)
which monitors the sales of over-the-counter healthcare products in
20,000 participating pharmacies in the states.
Survey of Early Warning Systems 5
The New York City Department of Health and Mental Hygiene
[Greenko 2003] has established a syndromic surveillance system since
2001 that monitors emergency department visits to provide early
detection of disease outbreaks. The key signs and symptoms analyzed
include respiratory problems, fever, diarrhea, and vomiting.
Concerns do exist for the effectiveness and general applicability
of syndromic surveillance [Stoto 2004]. In particular, the size and timing
of an outbreak for which syndromic surveillance gives an early
advantage may be limited. In a case involving hundreds or thousands of
simultaneous infections, no special detection methods would be needed.
Conversely, even the best syndromic surveillance system might not work
in a case involving only a few individuals such as the anthrax episodes of
2001 in the United States. Consequently, the size of an outbreak in
which syndromic surveillance can provide added value (on top and
beyond the traditional infectious disease surveillance) is probably on the
order of tens to several hundred people.
3. Reference Architecture for Model Extraction
Figure 1 illustrates the general reference architecture of an end-to-end
surveillance and response system. The surveillance module is responsible
for collecting multi-modal data from available data sources, and conduct
preliminary analysis based on one or more data sources. The
surveillance module works closely with the simulation and modeling
module to extract the model from these data sources. The primary
responsibility for the simulation and modeling module is to determine
whether an anomaly has already happened or is likely to happen in the
future. Furthermore, it is also responsible for interacting with the
decision maker to provide decision support on multiple what-if scenarios.
The decision maker can then use the command and control module to
launch appropriate actions (such as deploy antibiotics, applying ring
vaccination, and quarantine) based on the decisions.
6
C-S. Li
Figure 1: Reference architecture of an end-to-end surveillance & response system.
Surveillance and activity monitoring in environmental and public
health domain often involves (1) collecting data from clinical data
(patient records, billing information, lab results, etc.) as well as both
hardware and/or software sensors which generate multi-modal multi-
scale spatio-temporal data, (2) cleaning and preprocessing the data to
remove gaps and inconsistencies, if any, and (3) applying anomaly
detection methodologies to generate predictions and early warnings.
Predictions are often based on the environmental and public health threat
models.
As an example, we might subconsciously or consciously adjust our
diet when we feel ill (such as drinking more water, juice, and have more
rest). If the symptoms become more severe, we might seek over-the-
counter (OTC) medicine, and miss classes/work. In many cases, we
might go to work late or leave for home early. We might also experience
subtle change of our behavior at work. When the symptoms continue,
we might seek help from physicians. We usually have to make
appointments with the physicians (e.g. through phone or through web)
first. Physician visits often result in prescription medicines and thus
visits to the pharmacies.
Survey of Early Warning Systems 1
This behavior model suggests that we could potentially observe the
progression of a disease outbreak within a population at multiple touch
points by this model – such as sales of drinking water, sewage
generation, OTC drug sales, absentee information from school and work,
phone records to physician office, and 911 calls. Some of these data
may be collected before visits to the physician or hospital have actually
happened, and thus enable earlier detection. Data can also be collected
during and after visits to physicians have been made. These data could
include diagnosis made by the physician (including chief complaints),
lab tests, and drug prescriptions. Similar models can also be established
for pollution, non-infectious diseases, and other natural disasters.
We assume that the real world phenomenon, whether it is a disease
outbreak or an environmental event, will induce noticeable changes in
human, animal, or other environmental behaviors. The behavioral
change can be potentially captured from various hardware and/or
software sensors as well as traditional business transactions. The
challenge for early warning is to fuse those appropriate multi-modal and
multi-scale data sources to extract the behavior model of human or
environment and compared to the behavior under normal conditions (if
known) and declare the existence of anomaly when the behavior is
believed to be abnormal.
Figure 2 shows that the detection and early warning approaches in
environmental and public health application can be characterized along
three dimensions: problem domain, data sources, and detection
methodologies, each of which will be further elaborated in the following
three sections. These three dimensions are also the key aspects for
materializing the reference architecture shown in Fig. 1 for any specific
application. These three dimensions are often strongly correlated – as a
given problem domain (such as detecting influenza outbreak) will
dictates the available data sources and the most suitable detection
methodologies.
Figure 3 shows the reference architecture of a Health Activity
Monitoring system that materializes the multi-modal sense/surveillance
and modeling modules in Fig. 1. Data from various sources (both
traditional and non-traditional data) are streaming through the messaging
C.-S. Li
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Survey of Early Warning Systems 9
hub to anomaly detectors. A messaging hub is responsible for delivering
the messages and events from the publishers to the intended subscribers.
The publisher/subscriber clients allow the data to be streamed through
for any clients which subscribe to the specific data sources. Message
gateways can also be attached to the pub/sub clients for source-specific
data analysis before sending to the messaging hub.
Each anomaly detector can subscribe to one or more data sources, and
publish alerts for other anomaly detectors. The incoming data are also
sent into an operational database. An ETL (extract-transform-load)
module can periodically pull the data from the operational database into
a data warehouse for historical analysis. The analysis sometimes is
conducted with the help from a GIS server that stores the geographic
information. Additional statistical analysis can be performed on the
historical data by an analysis server. The public health personnel can
access alerts published in real time by the anomaly detectors as well as
use the analysis server and data warehouse to analyze the historical data.
Ontology and metadata (as shown in Fig. 3) for data sources can often
be used to assist in the interpretation of data at the appropriate
abstraction level. In the disease classification area, ICD-9-CM
(International Classification of Diseases, Ninth Revision, Clinical
Modification) is the official system of assigning codes to diagnoses and
procedures associated with hospital utilization in the United States. As
an example, diseases of the respiratory system are coded with 460-519.
New codes may be assigned to newly discovered diseases – such as
Severe Acute Respiratory Syndrome – SARS (480.3) has just been added
under the category of viral pneumonia (480) since 2003.
4. Problem Domain
The problem domains can be broadly classified according to the scale of
impact:
Non-infectious disease: such as cancer, cardiovascular disease,
dementia, and diabetes;
Infectious diseases: which include communicable diseases (such as
flu and smallpox, which can spread from human to human), vector-born
10 C.-S. Li
diseases which are carried by rodents or mosquitoes (such as West Nile
encephalitis, Dengue fever, malaria, and Hantavirus Pulmonary Disease).
Note that non-infectious diseases of a population can potentially have
a common root cause, such as caused by the same type of pollutant,
similar work condition, etc. Each of the problem domains can
potentially be associated with the progression of symptoms – such as
sore throat, running nose, coughing, fever, vomiting, dizziness, etc.
Most of the diagnoses done before the confirmation of lab tests are based
on apparent symptoms – and hence the term – syndromic surveillance.
The problem domain usually determines the data sources that will be
meaningful for early detection as well as which detection methods can be
applied. As an example, sewage data will be more useful for GI
(gastrointestinal) related disorders, while pollutants (from Environmental
Protection Agency – EPA) will be more useful for respiratory diseases or
disorders.
5. Data Sources
Data sources for early detection can be categorized into:
Clinically related data – the data acquired in a clinical setting such
as patient records (such as the reference information model defined by
HL7), insurance claims (e.g. CMS-1500 for physician visits and UB-92
for hospital visits), prescription drug claims (NCPDP), lab tests, imaging,
etc. These claim forms can be converted into an electronic format –
HEPAA 837 (HDPAA stands for Health Information Portability and
Accountability Act) and vice versa. As an example, CMS-1500 contains
information such as patient age, gender, geography, ICD-9 diagnosis
codes, CPT procedure codes, date of service, physician, location of care,
and payer type. NCPDP form for prescription drug contains, in addition
to the basic patient data, Rx date written, Rx date filled, NDC
(form/strength), quantity dispensed, days supply, specialty, payer type,
and pharmacy.
Non-traditional Data – Emerging syndromic surveillance
applications also start to use non-traditional (non-clinical) data sources to
Survey of Early Warning Systems 11
observe population behavior, such as retail sales (including over-the-
counter drug sales), absentee data from school and work, chief
complaints from the emergency room, and 911 calls. These data sources
do not necessarily have standardized formats. Additional data sources
include audio/video recording of seminars (for counting cough episodes).
Auxiliary Data – Additional data sources include animal data,
environmental data (ground moisture, ground temperature, and
pollutants) and micro-array data. Many of these data sources are
problem domain dependent.
A number of studies have been devoted to investigating various data
sources, such as the text and diagnosis code of the chief complaints from
emergency department [Begier 2003, Beitel 2004, Espino 2001, Greenko
2003], 911 calls [Dockrey 2002], and over-the-counter (OTC) drug sales
[Goldenberg 2002].
The data sources can be further characterized by its modality:
Structured: most of the transactional records stored in a relational
database belong to this category. Each field of a transaction is often well
defined. This may include a portion of the clinical & patient records –
such as patient name, visit date, care provider name and address,
diagnosis in terms of International Classification of Disease code (or
ICD-9 code).
Semi-structured: refers to data that has been tagged by mark up
languages such as XML. Emerging data standards such as HL7 enable
the transmission of healthcare related information in XML encoded
format.
Non-structured: Patient records, lab reports, emergency room
diagnosis and 911 calls could include chief complaints in free text
format. Additional non-structured data include data from various
instruments such as CT, PET, MRI, EKG, ultrasound and from clinical
and non-clinical data such as weather maps, videos, and audio segments.
The type of data sources is often essential in determining the
methodologies for detecting anomalies.
12 C.-S. Li
6. Detection Methods
The analytic methods are often data source dependent. Spatial scan
statistics has been most widely used, such as in [Berkom 2003]. Other
methods, including linear mixed models [Kleinman 2004], space-time
clustering [Koch 2001], CuSum [O’Brien 1997], time-series modeling
[Reis 2003], rule-based [Wong 2003], and concept-based [Buckridge
2002], have also been investigated and compared. A comprehensive
comparison among various detection algorithms is conducted in
[Buckridge 2005] as a result of the Darpa sponsored BioALIRT program.
The detection methods are used to determine the existence of
anomalies in the problem domain from available data sources, sometimes
with either explicit or implicit assumptions of models. These detection
methods, as shown in Fig. 2, can be categorized into:
Inductive method: Most of the statistical methods such as those
based on linear regression, Kalman filter, and spatial scan all fall into this
category. Inductive methods can be further categorized as supervised
and unsupervised methods. Supervised methods usually involve learning
and/or training a model based on historical data. Unsupervised methods,
on the other hand, do not require historical data for training.
Unsupervised methods are more preferable for those rare events (such as
those potentially caused by bio-terrorism) when there are insufficient
historical data. It has been concluded in [Buckridge 2005] that spatial
and other covariate information from disparate sources could improve
the timeliness of outbreak detection. Some of the existing syndromic
surveillance deployments such as the CDC BioSense and New York City
have leveraged both CuSum and Spatial Scan statistics.
Deductive methods: Deductive methods usually involve rule-based
reasoning and inferencing. This methodology is often used in the area
of knowledge-based surveillance in which existing pertinent knowledge
and data are applied in making inferences from the newly arrived data.
Hybrid inductive/deductive methods: Both inductive and deductive
methods can be used simultaneously on a given problem. Deductive
methods can be used to select the proper inductive method given the
prior knowledge in the problem domain and available data sources. This
Surrey of Early Warning Systems 13
often results in improved performance as compared to using either
inductive or deductive methods alone [Buckridge 2005].
7. Summary and Conclusion
Early warning systems for environmental and public health applications
have received substantial attention during the recent past due to increased
awareness of infectious diseases and availability of surveillance
technologies. In this chapter, we surveyed a number of existing early
warning systems in terms of their problem domains (non-infectious
disease vs. infectious disease), data sources (clinical data, non-traditional
data and auxiliary data), and detection approaches (inductive, deductive,
and hybrid). The rapid progress in the syndromic surveillance area
seems to suggest that early detection of certain infectious diseases is
feasible. Nevertheless, there is substantial interdependency among
problem domains, data sources, and detection methods for syndromic
surveillance. A validated early warning or anomaly detection approach
for a given problem area often cannot be generalized to other problem
areas due to the nature of data sources. Further studies in this area will
likely to be based on the ontology (or taxonomy) of the diseases, data
sources, and detection approaches.
Acknowledgment
The authors would like to acknowledge the EpiSPIRE bio-surveillance
team at IBM T. J. Watson Research Center. This research is sponsored
in part by the Defense Advanced Research Projects Agency and managed
by Air Force Research Laboratory under contract F30602-01-C-0184 and
NASA/IBM CAN NCC5-305.
The views and conclusions contained in this document are those of
the authors and should not be interpreted as necessarily representing the
official policies, either expressed or implied of the Defense Advanced
Research Projects Agency, Air Force Research Lab, NASA, or the
United States Government.
14
C.-S. Li
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I:i66-i75

 

This timely book identifies and highlights the latest data mining paradigms to analyze, combine, integrate, model and simulate vast amounts of heterogeneous multi-modal, multi-scale data for emerging real-world applications in life science. The cutting-edge topics presented include bio-surveillance, disease outbreak detection, high throughput bioimaging, drug screening, predictive toxicology, biosensors, and the integration of macro-scale bio-surveillance and environmental data with micro-scale biological data for personalized medicine. This collection of works from leading researchers in the field offers readers an exceptional start in these areas.


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