Data Science and Visualization in Health

Networks and Graphs

André Santanchè

Laboratory of Information Systems – LIS

Institute of Computing – UNICAMP

August 2025

Graphs?

Graph - Mathematical Model

nodes

edges

d

a

b

c

Why Graphs?

Graphs and the Real-world

Challenge

Select one example of a real-world problem and represent it as a graph.

Define:

• What are the nodes?
• What are the edges?

The Emergence of Network Maps

• Movie Actor Network, 1998
• World Wide Web, 1999
• C elegans neural wiring diagram 1990
• Citation Network, 1998
• Metabolic Network, 2000
• PPI network, 2001

Political/Financial Networks

Mark Lombardi: tracked and mapped global financial fiascos in the 1980s and 1990s from public sources such as news articles.

Mark Lombardi Industries Carlos Cardoen of Santiago, Chile c. 1982-90 (2nd Version) 2000

Understanding Through Visualization

"[...] Department of Homeland Security came in to take a look. They said they found the work revelatory, not because the financial and political connections he mapped were new to them, but because Lombardi showed them an elegant way to array disparate information and make sense of things, which they thought might be useful to their security efforts.[...]"

Michael Kimmelman�Webs Connecting the Power Brokers, the Money and the World�NY Times November 14, 2003

Understanding Through Visualization

"I happened to be in the Drawing Center when the Lombardi show was being installed and several consultants to the Department of Homeland Security came in to take a look. They said they found the work revelatory, not because the financial and political connections he mapped were new to them, but because Lombardi showed them an elegant way to array disparate information and make sense of things, which they thought might be useful to their security efforts. I didn't know whether to nd that response comforting or alarming, but I saw exactly what they meant.”

Michael Kimmelman�Webs Connecting the Power Brokers, the Money and the World�NY Times November 14, 2003

How Wolves Change Rivers

https://youtu.be/ysa5OBhXz-Q

• Yellowstone National Park
• Wolves→ Elks → Vegetation → Erosion

→ Water → Beavers

→ Dams → Fish

​

Les Miserables

(Neo4j example)

Modeling the World as Graphs

Models

Models

Data Storage

Data Management

Application

Application

Application

Conceptual

Model

Logic Model

Physical

Model

Models

Application

Application

Application

Conceptual

Model

membro:

Doriana

livro:

Dinolândia

empréstimo

abstraction

domain of discourse

universo de discurso

autor:

Horário

autoria

Models

Data Management

Application

Application

Application

Conceptual

Model

Logic Model

The Bridges of Königsberg

​

The Bridges of Königsberg

Task

​

• Draw a path where you can cross all the bridges, but each bridge only once.

Desenhe um caminho em que você seja capaz de cruzar todas as pontes, mas cada ponte apenas uma vez.

The Bridges of Königsberg

​

• Challenge
• cross each bridge only once
• Leonhard Euler in 1736
• proved that the problem has no solution

Bridges as a Graph

Bridges as a Graph

Conceptual

Model

Logic Model

Bridges as a Graph

• Degree of all nodes must be even
• except terminals (start/end)

Leonhard Euler in 1736

Simple

Principles

Complex

Systems

A Homogeneous Graph

The Eight Cities

Images generated by Gemini.

The Eight Cities

The Eight Cities as a Graph

• Nodes are cities
• Edges are roads
• All the cities have the same size and population
• All the roads have the same length

The Eight Cities as a Graph

Challenge

• Representing in Tables
• How do you represent a graph in a spreadsheet?
• You can use more than one tab

Models

Data Storage

Data Management

Application

Application

Application

Conceptual

Model

Logic Model

Physical

Model

Mapping Logical to Physical

Logical

Conceptual

Graph

Stored as a Graph

mapping

Mapping Logical to Physical

Logical

Conceptual

Graph

Stored as a Table

mapping

Graph - Mathematical Model

nodes

edges

d

a

b

c

Graph - Mathematical Model

• Graph
• pair of sets G=(V,E)

nodes - V

edges - E

d

a

b

c

Undirected Graph - Mathematical Model

• Graph
• pair of sets G=(V,E)
• Example
• V = {a, b, c, d}
• E = { {a,b}, {a,c}, {a,d}, {b,d}, {c,d} }

nodes - V

edges - E

d

a

b

c

Directed Graph - Mathematical Model

• Graph
• pair of sets G=(V,E)
• Example
• V = {a, b, c, d}
• E = { (a,b), (a,c), (d,a), (d,b), (d,c) }

nodes - V

edges - E

d

a

b

c

Undirected Graph - Adjacency Matrix

d

a

b

c

Directed Graph - Adjacency Matrix

d

a

b

c

Directed Graph - Edge List

d

a

b

c

The Eight Cities as a Graph

Challenge

• Representing in Tables
• How do you represent a graph in a spreadsheet?
• You can use more than one tab

Logical to Physical Model

Rot Donnadd

Pid Mught

Thulk Lebbimp

Bouvossam Damme

Pirg Zall

Logical to Physical Model

Rot Donnadd

Pid Mught

Thulk Lebbimp

Bouvossam Damme

Pirg Zall

Logical to Physical Model

Cytoscape

https://cytoscape.org/

Datasets

https://github.com/datasci4health/home/tree/master/data

Knowledge Graph

cell adhesion

cell-cell adhesion

cell-cell adhesion mediated by cadherin

cell-cell adhesion via plasma-membrane adhesion molecules

calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules

cellular process

biological process

developmental process

cell morphogenesis

Phenomena Graph

Knowledge Graph

cell adhesion

cell-cell adhesion

cell-cell adhesion mediated by cadherin

cell-cell adhesion via plasma-membrane adhesion molecules

calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules

cellular process

biological process

developmental process

cell morphogenesis

Machines talking to Machines

The Semantic Web�Machines talking to Machines

Berners-Lee, T., Hendler, J., & Lassila, O. (2001). The Semantic Web. Scientific American, 284(5), 28–37.

Case Study

Chronic Myeloid Leukemia (CML)

Philadelphia Chromosome

By Aryn89 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=37195209

Myeloid Stem Cell

By Cancer Research UK - Original email from CRUK, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=34334439

CML in a 4 years old female

By J3D3 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=47341095

Cell?

"Cell of Saint Teresa de Ávila in the Convent of Saint Joseph" (Wikipedia 2022)

​

"... is the process by which a cell uses its plasma membrane to engulf a large particle"

Cell?

"Cell of Saint Teresa de Ávila in the Convent of Saint Joseph" (Wikipedia, 2022)

​

"... is the process by which a cell uses its plasma membrane to engulf a large particle" (Wikipedia, 2022)

Explicit Semantics

Human Perspective

Machine Pattern Recognition

(e.g., by machine learning)

Semantic Web

Formal Knowledge

WordNet

Ontology

“An ontology is a formal, explicit specification of a shared conceptualisation.” (Studer et al., 1998)

Conceptualization

Formal, Explicit Specification

Ontology Spectrum

(Welty et al., 1999)

Starting from a Concept

Chronic Myeloid Leukemia (CML)

Connecting Concepts

Chronic Myeloid Leukemia (CML)

Leukemia

is a

Knowledge Graph

https://www.informatics.jax.org/disease/DOID:8552

Knowledge Graph

Chronic Myeloid Leukemia (CML)

Leukemia

is a

Knowledge Graph

Chronic Myeloid Leukemia (CML)

Leukemia

is a

concept

relationship between concepts

Concept

nucleous

Related Concepts

nucleous

intracellular anatomical structure

part of

Knowledge Graph

nucleous

intracellular anatomical structure

part of

concept

relationship between concepts

Knowledge Graph

https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005634

Tent of Miracles

Jorge Amado

author

Itabuna

bithPlace

DBPedia

recurso propriedade valor

Tent of Miracles author Jorge Amado

Jorge Amado birthPlace Itabuna

Knowledge Graph

(Ji et al., 2022)

Case Study

Human Symptom-Disease Network

Zhou, X., Menche, J., Barabási, A.-L., & Sharma, A. (2014). Human symptoms–disease network. Nature Communications, 5(1), 4212. https://doi.org/10.1038/ncomms5212

Clustered Regions - Same Disease Category

​

Downloading Datasets

https://doi.org/10.1038/ncomms5212

Downloading Datasets

https://doi.org/10.1038/ncomms5212

Diseases and Symptoms Table

TSV Dataset

https://github.com/datasci4health/datasci4health.github.io

Gene Ontology

mitochondrial DNA repair

GO:0043504

http://amigo.geneontology.org/amigo/term/GO:0043504

Ontologies

GO:0016055

Wnt signaling pathway

frizzled signaling pathway

Wnt signaling pathway

rdfs:label

obo:ExactSynonym

GO:0060071

Wnt signaling pathway, planar cell polarity pathway

taxon:9606

up:Q7Z3G6

up_core:organism

Prickle-like protein 2

rdfs:label

Homo sapiens

up_core:scientificName

rdfs:subClassOf

up_core:classifiedWith

Enrichment

Wang, Y., & Iha, H. (2023). The Novel Link between Gene Expression Profiles of Adult T-Cell Leukemia/Lymphoma Patients’ Peripheral Blood Lymphocytes and Ferroptosis Susceptibility. Genes, 14(11), 2005. https://doi.org/10.3390/GENES14112005

Chandak, P., Huang, K., & Zitnik, M. (2023). Building a knowledge graph to enable precision medicine. Scientific Data 2023 10:1, 10(1), 1–16. https://doi.org/10.1038/s41597-023-01960-3

Overview of PrimeKG

Downloading Datasets

PrimeKG Dataverse

https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/IXA7BM

CSV Dataset

https://github.com/datasci4health/datasci4health.github.io/tree/master/data/primekg

Task

Given this knowledge graph (PrimeKG), what kind of inferences can I make with it?

​

​

Dado este grafo de conhecimento (PrimeKG). Que tipo de inferências eu posso fazer com ele?

Phenomena Graph

Protein-Protein Interaction

Protein

Protein

Interaction

Case Study - Melanoma

Tables as Networks

Table to Graph

Nodes

Graph

Table

Graph

Table

node

prop1: value1

prop2:value2

prop3: value3

node

prop1: value1

prop2:value2

prop3: value3

Graph

Table

Graph

Table

:Protein

name: AKT1

identifier: 9606…28

:Protein

name: BRAF

identifier: 9606…60

Table to Graph

Edges

Graph

Table

node

node

edge

prop1: value1

prop2:value2

prop3: value3

Graph

Table

edge

experimental: 0.631

database: 0

:Protein

:Protein

name: AKT1

identifier: 9606…28

name: BRAF

identifier: 9606…60

Desnormalização

TSV Dataset

https://github.com/datasci4health/datasci4health.github.io

Database of known and predicted protein-protein interactions

https://string-db.org/

Search for Melanoma

​

Selecting Dataset

Selecting Dataset

CML in KEGG

CML in STRING

Labels

• Evidence:
• https://string-db.org/help//getting_started/#starting-point
• Scores:
• https://string-db.org/cgi/info?footer_active_subpage=scores

Showing just Experimental Physical Interactions

CML in STRING (Experimental Physical Interactions)

Exporting

https://github.com/datasci4health/datasci4health.github.io/tree/master/data/melanoma

CytoScape

Melanoma - CytoScape

Task

Given this protein interaction graph, what kind of analyses can I perform with it?

​

​

Dado este grafo de interação entre proteínas. Que tipo de análises eu posso fazer com ele?

Descoberta

Roads Flow

Castelo, Campinas (OpenStreetMaps, 2015)

Food Web - FishBase

Freshwater food web: Neo Martinez and Richard Williams.

(Cavoto et al., 2015)

Emergence

• Birds and Fishes
• Brain and Consciousness

​

Knowledge Graph

Phenomena Graph

Discovery

Inference

Our Approach

Discovery

Inference

References

• Cavoto, P., Cardoso, V., Lebbe, R. V., & Santanche, A. (2015). FishGraph: A network-driven data analysis. Proceedings - 11th IEEE International Conference on EScience, EScience 2015. https://doi.org/10.1109/eScience.2015.61

Acknowledgements

Image by eommina (https://pixabay.com/users/eommina-1183101/?utm_source=link-attribution&utm_medium=referral&utm_campaign=image&utm_content=2956377) from Pixabay (https://pixabay.com//?utm_source=link-attribution&utm_medium=referral&utm_campaign=image&utm_content=2956377 )

André Santanchè

http://www.ic.unicamp.br/~santanche/

License and Acknowledgements

• These slides are shared by a Creative Commons License, under the following conditions: Attribution, Noncommercial and Share Alike. See further details at https://creativecommons.org/licenses/by-nc-sa/4.0/
• Thanks to California Academy of Sciences [https://www.flickr.com/photos/casgeology/8981509235/] for its images adopted in the cover and background of the slides. See its specific license on the site.