1. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB:An Exploratory Data Science Platform
(A New Frontier: From Data Processing to Knowledge Exploration)
Mohammad Sadoghi
Assistant Professor
Department of Computer Science
Purdue University
IBM Cognitive Systems Institute Speaker Series
September 29, 2016

2. © 2016 Mohammad Sadoghi (Purdue University)
Insight is Lost in Islands of Data
2
http://www.cpsresearch.eu/clinical-trials/
http://news.mit.edu/2015/mnookin-vaccination-public-health-0227
http://www.healthcarepackaging.com/trends-and-issues/clinical-trials
http://stormercellularloo.gq/evolve-ii-clinical-trial.html
https://www.geneticliteracyproject.org
Data is spread across many islands of disconnected sources
(a lack of holistic view)

3. © 2016 Mohammad Sadoghi (Purdue University)
Insight is Lost in Islands of Data
3
http://www.cpsresearch.eu/clinical-trials/
http://news.mit.edu/2015/mnookin-vaccination-public-health-0227
http://www.healthcarepackaging.com/trends-and-issues/clinical-trials
http://stormercellularloo.gq/evolve-ii-clinical-trial.html
https://www.geneticliteracyproject.org
Sadly, adverse drug reactions (ADRs) is the 4th leading cause of
deaths in United States, resulting in100,000 loss of life annually

4. © 2016 Mohammad Sadoghi (Purdue University)
Insight is Lost in Islands of Data
4
http://www.cpsresearch.eu/clinical-trials/
http://news.mit.edu/2015/mnookin-vaccination-public-health-0227
http://www.healthcarepackaging.com/trends-and-issues/clinical-trials
http://stormercellularloo.gq/evolve-ii-clinical-trial.html
https://www.geneticliteracyproject.org
Adverse drug reaction costs over $136 billion dollars in US annually

5. © 2016 Mohammad Sadoghi (Purdue University)
Real-time Fusion and Exploration of Data

6. © 2016 Mohammad Sadoghi (Purdue University)
Real-time Fusion and Exploration of Enriched Data

7. © 2016 Mohammad Sadoghi (Purdue University)
Real-time Fusion and Exploration of Enriched Data at Web Scale

8. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
8
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
limit cells
growth
tum
or
suppressor
Why capture the semantic/context?
Semantic is essential to connect the dots.

9. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
9
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
limit cells
growth
tum
or
suppressor
Why capture the semantic/context?
Semantic is essential to connect the dots.

10. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
10
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
limit cells
growth
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
tum
or
suppressor
Why capture the semantic/context?
Semantic is essential to connect the dots.

11. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
11
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
limit cells
growth
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
tum
or
suppressor
?
Why capture the semantic/context?
Semantic is essential to connect the dots.

12. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
12
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
tum
or
suppressor
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
limit cells
growth
?
?
?
Why capture the semantic/context?
Semantic is essential to connect the dots.

13. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
13
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
(1) Instance Layer: Capturing raw data instances
including both structured & semi-structured data
How to capture the context?
limit cells
growth
tum
or
suppressor

14. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
14
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
How to capture the context?
limit cells
growth
tum
or
suppressor
(2) Relation Layer: Capturing the interconnectedness
of data instances across data sources

15. © 2016 Mohammad Sadoghi (Purdue University)
Drug Safety: Challenges of Real-time Fusion & Exploration of Open Data
15
PTGS2
(Gene)
inhibits
TP53
(Gene)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Naproxen
(Aleve)
Disease
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Methotrexate
DHFR
(Gene)
inhibits
Arthritis
Warfarin
Embolism
(Blood Clot)
Nicotine
VKORC1
(Gene)CYP2C9
(Enzyme)
Chemical
Carboxylic
Acids
Heterocyclic
Aminopterin
Phenylpro-
pionates
Approved
Drugs
increased
degradation
inhibits
Inhibits
Inhibits
Inhibits
How to capture the context?
limit cells
growth
tum
or
suppressor
(3) Semantic Layer: Capturing conceptual relationships
among data instances and their types

16. © 2016 Mohammad Sadoghi (Purdue University)
Enriched Data Model: Semantic is essential to connect the dots
16
PTGS2
(Gene)
TP53
(Gene)
Acetaminophen
(Tylenol)
Rheumatoid
Arthritis
Osteosarcoma
(Bone Cancer)
Relief
Fever
Ibuprofen
(Advil)
Immune
System
Autoimmune
Joint
Diseases
Sarcoma
Neoplasms
Drug Name Drug Targets
(Genes)
Symptomatic
Treatment
Ibuprofen PTGS2 Rheumatoid Arthritis
Acetaminophen PTGS2 Relief Fever
Methotrexate DHFR Antineoplastic
Anti-metabolite
Warfarin TP53 Embolism
(Blood Clot)
Gene Interaction
PTGS2 TP53 (Gene)
DrugBank: Bioinformatics & Cheminformatics Resource
CTD: Comparative Toxicogenomics Database
Gene Function
TP53 Tumor Suppressor
DHFR Limits Cell Growth
Uniprot: Universal Protein Resource
Gene Disease
TP53 Osteosarcoma
SemanticlayerRelationlayerInstancelayer
Methotrexate
DHFR
(Gene)
Arthritis
Warfarin
Embolism
(Blood Clot)
InformationKnowledgeData
Warfarin has narrow
therapeutic range
(fatal outcomes)
Dosage for Asians
population: 3.4 mg
Dosage for Whites
population: 5.1mg
Dosage for
African-Americans
population: 6.1 mg

17. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
17
Rank Query
Representation
Rank Query Refinement
Rank Data Sources Discovery
Rank Query Composition
Rank Query Answers
Rank Answer Evidence
Rank Answer
Representation
Query Refinement Ranking
Data Source Discovery Ranking
Query Composition Ranking
Query Answer Ranking
Evidence Ranking
Query
Representation Ranking
Answer Representation
Ranking
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
Yes/No

18. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
18
Rank Query
Representation
Rank Query Refinement
Rank Data Sources Discovery
Rank Query Composition
Rank Query Answers
Rank Answer Evidence
Rank Answer
Representation
Query Refinement Ranking
Data Source Discovery Ranking
Query Composition Ranking
Query Answer Ranking
Evidence Ranking
Query
Representation Ranking
Answer Representation
Ranking
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
Yes/No
“Is Warfarin sensitive to
ethnic background?”

19. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
19
Rank Query
Representation
Rank Query Refinement
Rank Data Sources Discovery
Rank Query Composition
Rank Query Answers
Rank Answer Evidence
Rank Answer
Representation
Query Refinement Ranking
Data Source Discovery Ranking
Query Composition Ranking
Query Answer Ranking
Evidence Ranking
Query
Representation Ranking
Answer Representation
Ranking
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
Yes/No
“Is Warfarin sensitive to
ethnic background?”
“Does Warfarin have a narrow
therapeutic range?”

20. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
20
Rank Query
Representation
Rank Query Refinement
Rank Data Sources Discovery
Rank Query Composition
Rank Query Answers
Rank Answer Evidence
Rank Answer
Representation
Query Refinement Ranking
Data Source Discovery Ranking
Query Composition Ranking
Query Answer Ranking
Evidence Ranking
Query
Representation Ranking
Answer Representation
Ranking
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
Yes/No
“Is Warfarin sensitive to
ethnic background?”
“Does Warfarin have a narrow
therapeutic range?”
“What are the disjoint classes of
population with respect to Warfarin?”

21. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
21
Rank Query
Representation
Rank Query Refinement
Rank Data Sources Discovery
Rank Query Composition
Rank Query Answers
Rank Answer Evidence
Rank Answer
Representation
Query Refinement Ranking
Data Source Discovery Ranking
Query Composition Ranking
Query Answer Ranking
Evidence Ranking
Query
Representation Ranking
Answer Representation
Ranking
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
Yes/No
“Is Warfarin sensitive to
ethnic background?”
“Does Warfarin have a narrow
therapeutic range?”
“What are the disjoint classes of
population with respect to Warfarin?”
“What are the adverse reactions
of Warfarin?”

22. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
22
Rank Query
Representation
Rank Query Refinement
Rank Data Sources Discovery
Rank Query Composition
Rank Query Answers
Rank Answer Evidence
Rank Answer
Representation
Query Refinement Ranking
Data Source Discovery Ranking
Query Composition Ranking
Query Answer Ranking
Evidence Ranking
Query
Representation Ranking
Answer Representation
Ranking
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
Yes/No
“Is Warfarin sensitive to
ethnic background?”
“Does Warfarin have a narrow
therapeutic range?”
“What are the disjoint classes of
population with respect to Warfarin?”
“What are the adverse reactions
of Warfarin?”
“What is an effective dosage of
Warfarin for preventing blood clot?”

23. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
23
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
“What are the disjoint
classes of population with
respect to Warfarin?”
“What is an effective
dosage of Warfarin for
preventing blood clot?”
“Does Warfarin have
a narrow therapeutic range?”

24. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
24
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
“What are the disjoint
classes of population with
respect to Warfarin?”
“What is an effective
dosage of Warfarin for
preventing blood clot?”
“Does Warfarin have
a narrow therapeutic range?”
Dosage for
African-Americans
population: 6.1 mg
Dosage for Whites
population: 5.1mg
Dosage for Asians
population: 3.4 mg

25. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
25
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
“What are the disjoint
classes of population with
respect to Warfarin?”
Querying different sources
return 6.1 mg, 5.1 mg, & 3.4 mg,
so is the data inconsistent?
(revisiting consistent answers formalism
& possible world semantics)
“What is an effective
dosage of Warfarin for
preventing blood clot?”
“Does Warfarin have
a narrow therapeutic range?”
Dosage for
African-Americans
population: 6.1 mg
Dosage for Whites
population: 5.1mg
Dosage for Asians
population: 3.4 mg

26. © 2016 Mohammad Sadoghi (Purdue University)
Context-aware Query Model
26
“Is 5.0 mg an effective dosage of Warfarin for preventing blood clot?”
“What are the disjoint
classes of population with
respect to Warfarin?”
Querying different sources
return 6.1 mg, 5.1 mg, & 3.4 mg,
so is the data inconsistent?
(revisiting consistent answers formalism
& possible world semantics)
“What is an effective
dosage of Warfarin for
preventing blood clot?”
“Does Warfarin have
a narrow therapeutic range?”
Dosage for
African-Americans
population: 6.1 mg
Dosage for Whites
population: 5.1mg
Dosage for Asians
population: 3.4 mg
Given the known narrow therapeutic range,
so is 5.1 mg close enough to 5.0 mg?
(fuzzy answers formalism in
presence of enriched data)

27. © 2016 Mohammad Sadoghi (Purdue University)
Spark Architecture: Knowledge Oblivious
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Immutable
Collection of
Objects)
Storage
Resource
Virtualization
27
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Apache Spark (General Data Processing on Distributed Memory)
Spark Data Model (Resilient Distributed Datasets — RDDs)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Personalized Medicine
(Drug Discovery/Safety)
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
Computational Finance
Compliance
Informatics

28. © 2016 Mohammad Sadoghi (Purdue University)
Spark Architecture: Knowledge Oblivious
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Immutable
Collection of
Objects)
Storage
Resource
Virtualization
28
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Apache Spark (General Data Processing on Distributed Memory)
Spark Data Model (Resilient Distributed Datasets — RDDs)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

29. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB Architecture: From Data to Knowledge
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
29
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Apache Spark (General Data Processing on Distributed Memory)
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

30. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB Architecture: From Data to Knowledge
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
30
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
Relation Layer Intra- & Inter-domain Linkage (fine-grained & instance-level)
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Apache Spark (General Data Processing on Distributed Memory)
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

31. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB Architecture: From Data to Knowledge
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
31
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
Semantic Layer Ontology Rules Stochastic Models Tensor Embedding
Relation Layer Intra- & Inter-domain Linkage (fine-grained & instance-level)
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Apache Spark (General Data Processing on Distributed Memory)
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

32. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB Architecture: From Data to Knowledge
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
32
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
Semantic Layer
Spark Data Model (RDDs) Generic Data Model (Key-Value Store)
Ontology Rules Stochastic Models Tensor Embedding
Relation Layer Intra- & Inter-domain Linkage (fine-grained & instance-level)
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Apache Spark (General Data Processing on Distributed Memory)
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

33. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB Architecture: From Data to Knowledge
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
33
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
ReasoningRefinementCuration Fusion Discovery
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Online Transactional Processing (OLTP) + Online Analytical Processing (OLAP)
Semantic Layer
Spark Data Model (RDDs) Generic Data Model (Key-Value Store)
Ontology Rules Stochastic Models Tensor Embedding
Relation Layer Intra- & Inter-domain Linkage (fine-grained & instance-level)
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

34. © 2016 Mohammad Sadoghi (Purdue University)
ExpoDB Architecture:Active Data Path
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
34
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
ReasoningRefinementCuration Fusion
Semantic Layer
Spark Data Model (RDDs) Generic Data Model (Key-Value Store)
Ontology Rules Stochastic Models Tensor Embedding
Discovery
Relation Layer Intra- & Inter-domain Linkage (fine-grained & instance-level)
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Virtualized Hardware Acceleration (GPU & FPGA)
Online Transactional Processing (OLTP) + Online Analytical Processing (OLAP)
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
Compliance
Informatics

35. © 2016 Mohammad Sadoghi (Purdue University)
Personalized Medicine
(Drug Discovery/Safety)
Computational Finance
The First Step!
Applications
APIs/Services
(Access/Interfaces)
Processing
Engine
Data Model
(Enriching Raw
Data Towards
Knowledge)
Storage
Resource
Virtualization
35
Spark
Streaming
SparkSQL
BlinkDB
GraphX SparkR MLlib
ReasoningRefinementCuration Fusion
Semantic Layer
Spark Data Model (RDDs) Generic Data Model (Key-Value Store)
Ontology Rules Stochastic Models Tensor Embedding
Discovery
Relation Layer Intra- & Inter-domain Linkage (fine-grained & instance-level)
Instance Layer Relational Graph/RDF Dense/Sparse MatricesJSON
Distributed File Systems (e.g., HDFS, S3, Ceph)
Distributed Memory (Tachyon)Compression (Succinct)
Resource Abstractions
(Apache Mesos)
Resource Management
(HadoopYarn)
Online Transactional Processing (OLTP) + Online Analytical Processing (OLAP)
L-Store
(Real-time OLTP+OLAP)
FQP
(Flexible Query Processor)
EmbedS
(Ontology)
Phenomenological Features
(Deep-Learning-as-Oracle)
PADRES
(Event Processing)
IBM DB2 BLU
(Column Store)
SPIDER
(Declarative Data Cleansing)
Vraph
(Vectorized Graph Processing)
Tiresias
(Predicting Adverse Drug Reaction)
fpga-ToPSS
(Algorithmic Trading)
Compliance
Informatics
Virtualized Hardware Acceleration (GPU & FPGA)

36. © 2016 Mohammad Sadoghi (Purdue University)
ThankYou
Q&A
Exploratory Systems Lab (ExpoLab)
website: https://msadoghi.github.io/

37. © 2016 Mohammad Sadoghi (Purdue University)
Data/Knowledge Exploration:
• Mohammad Sadoghi, Kavitha Srinivas, Oktie Hassanzadeh,Yuan-Chi Chang, Mustafa Canim,Achille Fokoue,Yishai A. Feldman: Self-Curating Databases. EDBT 2016
• Amit Chandel, Oktie Hassanzadeh, Nick Koudas, Mohammad Sadoghi, Divesh Srivastava: Benchmarking declarative approximate selection predicates. SIGMOD Conference 2007: 353-364
• Oktie Hassanzadeh, Mohammad Sadoghi, Renée J. Miller:Accuracy of Approximate String Joins Using Grams. QDB 2007
Drug Safety:
• Achille Fokoue, Mohammad Sadoghi, Oktie Hassanzadeh, Ping Zhang: Predicting Drug-Drug InteractionsThrough Large-Scale Similarity-Based Link Prediction. ESWC 2016
• Achille Fokoue, Oktie Hassanzadeh, Mohammad Sadoghi, Ping Zhang: Predicting Drug-Drug InteractionsThrough Similarity-Based Link Prediction OverWeb Data.WWW 2016
OLTP & OLAP:
• Mohammad Sadoghi, Souvik Bhattacherjee, Bishwaranjan Bhattacharjee, Mustafa Canim: L-Store:A Real-time OLTP and OLAP System. CoRR abs/1601.04084 (2016)
• Kaiwen Zhang, Mohammad Sadoghi, Hans-Arno Jacobsen: DL-Store:A Distributed Hybrid OLTP and OLAP Data Processing Engine. ICDCS 2016
• Mohammad Sadoghi, Kenneth A. Ross, Mustafa Canim, Bishwaranjan Bhattacharjee: Exploiting SSDs in operational multiversion databases.VLDB J. 25(5): 651-672 (2016)
• Mohammad Sadoghi, Mustafa Canim, Bishwaranjan Bhattacharjee, Fabian Nagel, Kenneth A. Ross: Reducing Database Locking ContentionThrough Multi-version Concurrency. PVLDB 7(13):
1331-1342 (2014)
• Prashanth Menon,Tilmann Rabl, Mohammad Sadoghi, Hans-Arno Jacobsen: CaSSanDra:An SSD boosted key-value store. ICDE 2014: 1162-1167
• Prashanth Menon,Tilmann Rabl, Mohammad Sadoghi, Hans-Arno Jacobsen: Optimizing key-value stores for hybrid storage architectures. CASCON 2014: 355-358
• Mohammad Sadoghi, Kenneth A. Ross, Mustafa Canim, Bishwaranjan Bhattacharjee: Making Updates Disk-I/O Friendly Using SSDs. PVLDB 6(11): 997-1008 (2013)
Hardware Acceleration:
• Rajesh R. Bordawekar, Mohammad Sadoghi:Accelerating database workloads by software-hardware-system co-design. ICDE 2016
• Mohammadreza Najafi, Mohammad Sadoghi, Hans-Arno Jacobsen: SplitJoin:A Scalable, Low-latency Stream Join Architecture with Adjustable Ordering Precision. USENIX AnnualTechnical
Conference 2016
• Mohammadreza Najafi, Mohammad Sadoghi, Hans-Arno Jacobsen:The FQPVision: Flexible Query Processing on a Reconfigurable Computing Fabric. SIGMOD Record 44(2): 5-10 (2015)
• Mohammadreza Najafi, Mohammad Sadoghi, Hans-Arno Jacobsen: Configurable hardware-based streaming architecture using Online Programmable-Blocks. ICDE 2015
• Mohammedreza Najafi, Mohammad Sadoghi, Hans-Arno Jacobsen: Flexible Query Processor on FPGAs. PVLDB 6(12): 1310-1313 (2013)
• Mohammad Sadoghi, Rija Javed, NaifTarafdar, Harsh Singh, Rohan Palaniappan, Hans-Arno Jacobsen: Multi-query Stream Processing on FPGAs. ICDE 2012: 1229-1232
• Mohammad Sadoghi, Harsh Singh, Hans-Arno Jacobsen:Towards highly parallel event processing through reconfigurable hardware. DaMoN 2011: 27-32
• Mohammad Sadoghi, Harsh Singh, Hans-Arno Jacobsen: fpga-ToPSS: line-speed event processing on fpgas. DEBS 2011: 373-374
• Mohammad Sadoghi, Hans-Arno Jacobsen, Martin Labrecque,Warren Shum, Harsh Singh: Efficient Event Processing through Reconfigurable Hardware for AlgorithmicTrading. PVLDB 3(2):
1525-1528 (2010)
References: