Maio 2018 Institute of Computing – UNICAMP Laboratory of...
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Data Science and Simulation for Health Learning Ciência dos Dados e Simulação para Aprendizado em Saúde André Santanchè Laboratory of Information Systems – LIS Institute of Computing – UNICAMP Maio 2018
Transcript of Maio 2018 Institute of Computing – UNICAMP Laboratory of...
Data Science and Simulation for Health Learning
Ciência dos Dados e Simulação para Aprendizado em Saúde
André SantanchèLaboratory of Information Systems – LIS
Institute of Computing – UNICAMPMaio 2018
Zombie Health
Facts● Blood test
○ 20% die
● Bacterial Infection - Cyanobacterium zumbi○ without treatment 95% die○ death in 4 days
● Viral infection○ without treatment 60% die○ death in 8 days
● There is no recurrence of the same kind of infection● Wrong treatment kill the zombie
Part 1
Boorthoo Tieppaeth● yellow tong
Boorthoo Tieppaeth● yellow tong● trembling on the little finger
Boorthoo Tieppaeth● yellow tong● trembling on the little finger
bite deficit
Boorth Teppeeth● yellow tong
Boorth Teppeeth● yellow tong● paralysis
Boorth Teppeeth● yellow tong● paralysis
bacterial infection
Aubuthu Teppeeth● trembling on the little finger
Aubuthu Teppeeth● trembling on the little finger
bite deficit
Read Rait● chest pain
Read Rait● chest pain● history?
Read Rait● chest pain● history: bacterial infection
viral infection
Tasha Baba● chest pain● purple tong
Tasha Baba● chest pain● purple tong● options:
○ treat as virus○ blood test○ do not treat
Tasha Baba● chest pain● purple tong
viral infection
Tasha Baba● chest pain● purple tong● options:
○ treat as virus - die if it is not virus (25% chance)○ blood test - 20% die○ do not treat - 60% die if it is virus (75% chance)
Symptoms● Bacterial Infection - Cyanobacterium zumbi
○ yellow tong - since the 1st day (100% cases)○ paralysis - from the 2nd day (100% cases)○ chest pain - from the 5th day (10% cases)
● Bite deficit○ yellow tong - from the 5th day (100% cases)○ trembling on the little finger - from the 3rd day (90% cases)○ member loss - from the 10th day (100% cases)
● Viral infection○ chest pain - from the 2nd day (100% cases)○ member loss - from the 5th day (100% cases)
● Viral + Bacterial Infection○ member loss - 1st day (20% cases)
Jacinto Bemelhor
StartJacinto Bemelhor
▪Moodle-based Game
▪ Successful experience
▪Engagement of professors and students
SchemaGrangeia, T. de A. G., Jorge, B. de, Franci, D., Santos, T. M., Setubal, M. S. V., Schweller, M., & Carvalho-Filho, M. A. de. (2016). Cognitive Load and Self-Determination Theories Applied to E-Learning: Impact on Students’ Participation and Academic Performance. PLOS ONE, 11(3), e0152462. https://doi.org/10.1371/journal.pone.0152462
Social Engagement Platform
Jacinto Bemelhor
Text
Comments
TextTextDecisions
EducatorsStudents
Jacinto Actual ModelText
Comments
TextTextDecisions
EducatorsStudents
Assumptions
New Generation Platform● Interactive game design● More autonomy for machines to
○ conduct the game○ evaluate and give feedback
● Knowledge-base approach○ Hypothesis:
■ cases can be decomposed in smaller elements■ elements can be combined to produce diversity
○ The system can tailor the route according to the student
New Generation Platform● Easier to feed with new cases (long term)● Fine-grained progress tracking and evaluation● Educators can
○ spend time in higher level interaction○ better monitor students○ scale-up their time
Text-based PlatformText
Text Text
Decision
DecisionDecision
Text Text Text
Knowledge-base Game
Text
Comments
TextTextDecisions
Knowledge-base
Engine
Knowledge-baseUnderestimated Problem
Histórico
Sinaisvitais
Medicamentos
Exames
Paciente
DoençasDispneia
AsmaMedicamentosInalação com
feneterol
Doenças
ManifestaçõesSintomas
SintomasDificuldade para falar
Chiado no peitoFalta de ar
DoençaDispneia
GêneroMasculino
Faixa de idade25-40
AcompanhadoSim
EstadoAlerta
Falta de ar(dispneia)
Chiado no peito
Dificuldade para falar
DeCS / MeSH: A- Descritores em Inglês, Espanhol, Português – B- Descrição, C- Sinônimos, D- Categorias,
E- Qualificadores, F- Registros, G- Identificadores
?
DeCS / MeSH: A- Resp. Sounds, Ruidos Resp., Sons Resp. -B-…, C-(Lung Sound, Rhonchi, Wheezing,...), D-(Signs and Symp.,
Diag. Techn., Resp. Phys. Phen., ...), E-(IM, DI, DE, …), F-(27799), G-(D012135)
DeCS / MeSH: A- Dyspnea, Disnea, Dispneia -B- Labored breathing, C- Shortness of breath, D- (Signs and Symp.,
Resp. Disorders), E-(IM, DI, PP, …), F-(27799), G-(D004417)
Duração1 dia
IntensidadeAlta
Duração1 dia
IntensidadeAlta
Dispneia(falta de ar)
Asma
Inalação comfenoterol
Internist-I EVOKS,IMPORT, FREQ
Pressão ArterialPA=142x88mmHg
Freq. CardíacaFC=126bpmFreq. Resp.FR =34rpm
Oxim. PulsoSpO2=93%
Temperatura36,8oC
Pico de fluxoexpiratório
27% do previsto
Traqueiacentrada
Murmúrio vesicularreduzido glob. e bilat.Retração de fúrcula
Respiratórios
Bulhas cardíacas hipofonéticas
DeCS / MeSH: A- Asthma, Asma, Asma -B- ..., C- Bronchial Asthma, D- (Bronchial Diseases, Lung Dis., Repir. Hypersens.), E-(PP, VI, SU, …), F-(1257), G-(D001249)
Knowledge Base
Complexity and Reductionism
Scientific Reduction● "The term ‘reduction’ as used in philosophy expresses the idea that if an
entity x reduces to an entity y then y is in a sense prior to x, is more basic than x, is such that x fully depends upon it or is constituted by it."
● "Saying that x reduces to y typically implies that x is nothing more than y or nothing over and above y."
(van Riel, Raphael and Van Gulick, 2016)
Emergence● “[…] emergence is a process whereby larger entities, patterns, and
regularities arise through interactions among smaller or simpler entities that themselves do not exhibit such properties.” (Wikipedia, 2015)
● “emergent entities (properties or substances) ‘arise’ out of more fundamental entities and yet are ‘novel’ or ‘irreducible’ with respect to them.” (O'Connor, 2012)
Emergence - Examples● Birds and Fishes● Brain and Consciousness● Water
How Doctors Act and Learn?
How does a Doctor "see" a Patient?
Differential Diagnosis"a type of analytical task wherein the decision maker is confronted with a fixed set of diagnostic alternatives. His job is to determine whether sufficient data are available to make a decision among elements of this set and if not, to obtain whatever additional data may be required to make a decision." (Pople, 1982)
Causal Reasoning"Causal reasoning in science relies on the premise that for each observed phenomenon, there exists an underlying mechanism that links cause and effect." (Sobolev, 2012)
Complexity
Physics and Biology SciencesEntre vivos e inanimadosWilliam Bialek
Bialek, W. (2018). Entre vivos e inanimados. Revista Pesquisa FAPESP, 72–74. Retrieved from http://revistapesquisa.fapesp.br/2018/03/20/william-bialek-entre-vivos-e-inanimados/
● Same notion to Exact and Natural Sciences?
Knowledge FlowAncient Times
CausalityExplicit - Snake Bite
CausalityExplicit - Snake Bite
CausalityExplicit - Snake Bite
CausalityComplex - Arrhythmia
CausalityComplex - Arrhythmia
Knowledge FlowClinical Cases
Knowledge FlowAncient Times
ClinicalCases
Individual experience
Individual experience
Knowledge FlowAncient Times
ClinicalCases
Individualexperience
Individualexperience
Collectiveexperience
Collectiveexperience
Knowledge FlowAncient Times
ClinicalCases
Individualexperience
Individualexperience
Collectiveexperience
Collectiveexperience
Writing
By Alphabets alphabetical - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=39702181
The Ancient Healer● "the notable ancient Egyptian healer, [...], is known to have treated surface
infections with mouldy bread."● "Holy-men of central Asia also prepared a paste made from chewed barley
and apple which, when mouldy, was used as a poultice on surface wounds."
(Wainwright, 1989)
Knowledge FlowNowadays
Research
Articles
Unveiling Mechanisms(Marieb & Keller, 2017)
Knowledge FlowClinical Cases
Knowledge FlowClinicalCases
Knowledge Flow
ElectronicHealthRecords
ClinicalCases
Knowledge FlowArticles
ClinicalCases
ElectronicHealthRecords
Knowledge Flow
ElectronicHealthRecords
ClinicalCases
Articles
Articles
Knowledge Flow
ElectronicHealthRecords
ClinicalCases Articles
Articles
Knowledge Flow
ElectronicHealthRecords
ClinicalCases Articles
Articles
Meta-Analysis
Knowledge Flow
ElectronicHealthRecords
ClinicalCases Articles
Articles
Guidelines& Pathways
Review of the NICE guidance on bacterial meningitis and meningococcal septicaemia(Radcliffe, 2011)
NICEhttps://pathways.nice.org.uk/pathways/bacterial-meningitis-and-meningococcal-septicaemia-in-under-16s
NICEhttps://pathways.nice.org.uk/pathways/heart-rhythm-conditions/heart-rhythm-conditions-overview#content=view-node:nodes-ventricular-arrhythmias
Knowledge Flow
ElectronicHealthRecords
ClinicalCases Articles
Articles
Meta-Analysis
Guidelines& Pathways
Knowledge Flow
ElectronicHealthRecords
ClinicalCases
Knowledge Flow
ElectronicHealthRecords
ClinicalCases Articles
Articles
Meta-Analysis
Guidelines& Pathways
Zombie Health and Weka
Health Data Science
Doctors Thinking Process"[...] thinking processes are based on the complex interconnection of signs and symptoms presented by the patient that are aggregated in the physician’s mind through a complex hierarchical chain of interconnections."
"Traditionally, doctors used to learn to value these signs and symptoms without a scientific approach based on their real epidemiology, but relying on a repository of collective memories."
Marco Antonio de Carvalho Filho in (Mota et al., 2018)
Evidence-based Medicine (EBM)"[...] movement aiming at increasing the use of conscientious and rational clinical decision making, emphasizing the use of evidence from previous, reliable and well-conducted research. (Shaughnessy et al., 2016) (Rosenberg & Donald, 1995)"
"Nowadays, EBM is the best approach to developing a therapeutic plan to a patient, since it comprises the best evidence, patient values, and personal characteristics together with clinical experience."
Marco Antonio de Carvalho Filho in (Mota et al., 2018)
Evidence-based Medicine
(Panju et al., 1998)
Fourth Paradigm - Exact and Natural Sciences"Bialek afirma que os fenômenos do mundo vivo são suscetíveis aos experimentos quantificativos da física" (Bialek, 2018)
The Fourth Paradigm(Gray, 2007)
● "Thousand years ago: science was empirical;describing natural phenomena
● Last few hundred years: theoretical branch;using models, generalizations
● Last few decades: a computational branch;simulating complex phenomena
● Today: data exploration (eScience)unify theory, experiment, and simulation
○ Data captured by instruments or generated by simulator○ Processed by software○ Information/knowledge stored in computer○ Scientist analyzes database/ files using data management and statistics"
(Holzinger, 2014)Scales
Dimensions
Diversity
Dep
th
Dimensions
Diversity -> Catalogs
Dep
th ->
Des
crip
tions
Limited View of EHRs
(Shortliffe & Cimino, 2014)
Learning Health Care
System
(Shortliffe & Cimino, 2014)
Learning Health Care System"This notion of a system that allows us to learn from what we do, unlocking the experience that has traditionally been stored in unusable form in paper charts, is gaining wide attention now that we can envision an interconnected community of clinicians and institutions, building digital data resources using EHRs. The concept has been dubbed a learning health care system [...]" (Shortliffe & Cimino, 2014)
How to Learn in Modern Times?
Flexnerian Education“the actual practice of health care education remains primarily a Flexnerian one of science-based acquisition of medically relevant knowledge, followed by on-the-job apprentice-style acquisition of experience, and accompanied by evolution and expansion of the curriculum to add new fields of knowledge (Flexner 1910 ).” (Shortliffe & Cimino, 2014)
Problem-based Learning“In the 1960s, McMaster University in Canada pioneered a new approach, problem-based learning , where small groups of students, supported by a facilitator, learned through discussion of individual case scenarios (Neville 2009 ).” (Shortliffe & Cimino, 2014)
Problem-based Approach“This problem-based approach was proposed as an alternative to didactic lectures, supporting individualized learning, and placing this learning in the context of the patient rather than the context of a single discipline.” (Shortliffe & Cimino, 2014)
Problem-based Learning
Ensino Baseado em Projetos
▪Problem Based Learning (PBL)
▪Case Based Learning (CBL)
▪WebQuest
Problem-based Learning
▪“uma estratégia instrucional em que estudantes se confrontam com problemas contextualizados e pouco estruturados e empenham-se em encontrar soluções significativas.” (Rhem, 1998)
Simulation
Simulation and Education“In a report on educational technology to the President of the USA, a committee of science advisors presented the most promising constructivist applications of technology, with simulations on top of the list.” (Repenning et. al, 1999)
Tradução: “Em um relatório sobre tecnologia educacional para o Presidente dos Estados Unidos, um comitê de consultores científicos apresentaram as mais promissoras aplicações construtivistas da tecnologia, com simulações no topo da lista.” (Repenning et. al, 1999)
Patient Simulation
Mannequin
https://commons.wikimedia.org/wiki/File:Human_Patient_Simulation.jpg
Control WindowLaerdal SimMan
(Takeuchi et al., 2012)
Scenario EditorLaerdal SimMan
(Takeuchi et al., 2012)
Document Case Descriptions
Document Case Descriptions
▪Free Cases▫ http://healthysimulation.com/5805/free-simulation-faculty-training-tools-scenarios-from-uw/
▪EM Sim Cases▫ https://emsimcases.com
▪ thesimtech▫ http://thesimtech.com
Graph Scenarios
Tasha Baba● chest pain● purple tong
Tasha Baba● chest pain● purple tong● options:
○ treat as virus○ blood test○ do not treat
Tasha Baba● chest pain● purple tong
viral infection
Tasha Baba● chest pain● purple tong● options:
○ treat as virus - die if it is not virus (25% chance)○ blood test - 20% die○ do not treat - 60% die if it is virus (75% chance)
The Map
Health Profile
Textual
OpenLabyrinthhttp://vp.openlabyrinth.ca/renderLabyrinth/index/55
Health Profile
Rich Media
The New England Journal of Medicinehttp://www.nejm.org/multimedia/interactive-medical-case
Health Profile
Rich Media
The New England Journal of Medicinehttp://www.nejm.org/multimedia/interactive-medical-case
Health Profile
Structured
Control Window - Laerdal SimMan(Takeuchi et al., 2012)
Catherine Millerhttps://labyrinth.sgul.ac.uk/mnode.asp?id=qgxlrdbu3lpfvf4jesngxlrdbtpr9kq
Aplications
The New England Journal of Medicinehttp://www.nejm.org/multimedia/interactive-medical-case
Continuum of Competency
(Cook & Triola, 2009)
How Games could Help?
Máquinas jogando xadrez
1997Deep Blue beats Garry Kasparov
world chess champion
Pessoas passam a jogar contra Máquinas
Qual a diferença de aprender xadrez em livros e jogando?
Por que é importante ir para um país de língua inglesa para aprender inglês?
Qual o ambiente natural para o seu cérebro aprender a língua?
Qual o ambiente natural para o seu cérebro aprender xadrez?
LOGOAprendendo matemática na
“Matelândia”- Seymour Papert
Xadrez na “Xadrelândia”
Computers Push Humans to Excel At Playing Chess
Christopher Chabris & David GoodmanThe Wall Street Journal, 2013
Aprendendo com as Máquinas
▪“But players have learned from computers that some kinds of chess positions are playable, or even advantageous, even though they might violate general principles.” (Chabris & Goodman, 2013)
Crescimento
▪“1,500 grandmasters, more than twice as many as in 1997”
▪“Twenty-two of them earned the title before reaching the age of 15”
(Chabris & Goodman, 2013)
Ratingacima de 2.700
▪“1971, the only player rated over 2,700 was Bobby Fischer”
▪“Even by 1997 there were just eight.”▪“Nowadays an entire website is dedicated to
tracking the 50 or so players who on any given day are rated 2,700 or higher.”
(Chabris & Goodman, 2013)
Our Research
More Autonomy to Machines to
▪Conduct the game
▪Evaluate and give feedback
▪Guide the student
Long Term Goals
▪Easier to feed with new cases
▪Machines can synthesize new cases or fill gaps of existing cases
▪ System will tailor the route according to the student
Educator will
▪ Spend time in higher level interaction
▪Better monitor students
▪ Scale-up their time
Arch
itec
ture
Architecture
Architecture
Knowledge-base Challenges● Data extraction from health documents● Representation of medical knowledge● Clinical scenarios representation, including symptoms, diseases and
interventions
Extraction
Sources of Data● Databases of Health Care Institutions● Public Health Databases● Scientific Articles
○ EBM Articles
● Guidelines and Pathways● Existing Cases● Dictionaries, Thesaurus and Ontologies
Learning Health Care
System
(Shortliffe & Cimino, 2014)
NICEhttps://pathways.nice.org.uk/pathways/heart-rhythm-conditions/heart-rhythm-conditions-overview#content=view-node:nodes-ventricular-arrhythmias
Evidence-based Medicine
(Panju et al., 1998)
How to identify, extract and convert relevant data from data sources?
● Diseases● Symptoms● Interventions and Treatments● Medications● Outcomes
Knowledge Representation
Internist I(First et al., 1985)
Internist I(First et al., 1985)
Bayesian Representation(Combs et al., 2016)
Graph Knowledge Base
Scaling and Tailoring
Automatic Evaluation▪How to automatically compare the student track
with the suggested track?▪How to automatically evaluate the track?
▪How to give feedback?
Scaling and Tailoring
Case Synthesis▪ Is it possible to synthesize:
▫ trustable variable values to fill the gaps in existing cases?
▫ new trustable cases combining previous ones?
Fuzzy Logic and Networks
Graph Knowledge Base
References● Bialek, W. (2018). Entre vivos e inanimados. Revista Pesquisa FAPESP, 72–74. Retrieved from
http://revistapesquisa.fapesp.br/2018/03/20/william-bialek-entre-vivos-e-inanimados/● Chabris, C., & Goodman, D. (2013). Computers Push Humans to Excel At Playing Chess. The
Wall Street Journal.● Combs, C. D., Sokolowski, J. A., & Banks, C. M. (Eds.). (2016). The Digital Patient : Advancing
Healthcare, Research, and Education. New Jersey: John Wiley & Sons.● Cook, D. A., & Triola, M. M. (2009). Virtual patients: a critical literature review and proposed
next steps. Medical Education, 43(4), 303–311.● First, M. B., Soffer, L. J., and Miller, R. A. (1985). QUICK (QUick Index to Caduceus Knowledge):
Using the Internist-1/Caduceus knowledge base as an electronic textbook of medicine. Computers and Biomedical Research, 18(2):137–165.
References● Grangeia, T. de A. G., Jorge, B. de, Franci, D., Santos, T. M., Setubal, M. S. V., Schweller, M., &
Carvalho-Filho, M. A. de. (2016). Cognitive Load and Self-Determination Theories Applied to E-Learning: Impact on Students’ Participation and Academic Performance. PLOS ONE, 11(3), e0152462. https://doi.org/10.1371/journal.pone.0152462
● Gray, J. (2007). Jim Gray on eScience: A Transformed Scientific Method. In T. Hey, S. Tansley, & K. Tolle (Eds.), The Fourth Paradigm. Redmond: Microsoft Research.
● Marieb, E. N., & Keller, S. M. (2017). Essentials of human anatomy & physiology. Pearson Education.
References● Mota, Matheus Silva, Filho, Francisco José Nardi, Horvat, Roger Vieira, Schweller, Marcelo,
Grangeia, Tiago de Araujo Guerra, Filho, Marco Antonio de Carvalho, Reis, Júlio Cesar dos, Pantoja, Fagner Leal, Santanchè, André. (2018) Multiscaling a Finding-Disease Dataspace . (under review)
● O'Connor, Timothy and Wong, Hong Yu, (2012) Emergent Properties, The Stanford Encyclopedia of Philosophy (Spring 2012 Edition), Edward N. Zalta (ed.), URL = <http://plato.stanford.edu/archives/spr2012/entries/properties-emergent/>.
● Panju, A. A., Hemmelgarn, B. R., Guyatt, G. H., & Simel, D. L. (1998). Is this patient having a myocardial infarction? JAMA, 280(14), 1256–1263.
References● Pople Jr., H. E. (1982). Heuristic Methods for Imposing Structure on Ill-Structured Problems:
The Structuring of Medical Diagnostics. In Artificial Intelligence in Medicine (Vol. 51). Boulder: Westview Press.
● Radcliffe, R. H. (2011). Review of the NICE guidance on bacterial meningitis and meningococcal septicaemia. Archives of Disease in Childhood. Education and Practice Edition, 96(6), 234–7. https://doi.org/10.1136/archdischild-2011-301019
● Repenning, Alexander & Ioannidou , Andri & Phillips, Jonathan. Collaborative Use & Design of Interactive Simulations. Proceedings of Computer Supported Collaborative Learning Conference at Stanford (CSCL'99), 1999 [Online] http://www.escot.org/External/UseDesign.pdf
● Rhem, James (1988). Problem-Based Learning: An Introduction. Vol. 8.● Shortliffe, E. H., & Cimino, J. J. (Eds.). (2014). Biomedical Informatics - Computer Applications
in Health Care and Biomedicine. London: Springer London.
References● Sobolev, B., Sanchez, V., & Kuramoto, L. (2012). Health Care Evaluation Using Computer
Simulation. Boston, MA: Springer US.● Takeuchi, A., Kobayashi, T., Hirose, M., Masuda, T., Sato, T., & Ikeda, N. (2012). Arterial pulsation
on a human patient simulator improved students’ pulse assessment. Journal of Biomedical Science and Engineering, 5(5), 285–289. http://doi.org/10.4236/jbise.2012.55036
● van Riel, Raphael and Van Gulick, Robert. (2016). Scientific Reduction, The Stanford Encyclopedia of Philosophy (Winter 2016 Edition), Edward N. Zalta (ed.), URL = <https://plato.stanford.edu/archives/win2016/entries/scientific-reduction/>.
● Wainwright, M. (1989). Moulds in ancient and more recent medicine. Mycologist, 3(1), 21–23. https://doi.org/10.1016/S0269-915X(89)80010-2
André Santanchèhttp://www.ic.unicamp.br/~santanche/teaching/ehealth/
License and AcknowledgementsThese 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 2500529 [https://pixabay.com/en/users/2500529-2500529/] for her/his image "Digitization the Background Technology" [https://pixabay.com/en/digitization-the-background-1599552/] adopted in the background of the slides. See its specific license on the site.
Thanks to Julie M [https://pixabay.com/en/users/mcmurryjulie-2375405/] for her image "Person from Dots Personalized" [https://pixabay.com/en/person-from-dots-2307944/] adopted in the background of the slides. See its specific license on the site.
