The great barrier to AI adoption in healthcare and biomedical research is lack of trust.
Assessing trustworthiness requires data, domain and user context, which can be supported by ontologies, knowledge graphs and FAIR data.
Deep learning for biomedical discovery and data mining IIDeakin University
(1) The document discusses deep learning techniques for analyzing biomedical data from electronic medical records (EMRs).
(2) It describes models like DeepPatient that use autoencoders to learn representations of patient records that can predict diseases.
(3) Other models like Deepr and DeepCare use convolutional and recurrent neural networks to model temporal patterns in EMRs and predict future health risks and care trajectories.
Prospects of Deep Learning in Medical ImagingGodswll Egegwu
A SEMINAR Presentation on the Prospects of Deep Learning in Medical Imaging Presented to the Department of Computer Science, Nasarawa State Polytechnic, Lafia.
BY:
EGEGWU, GODSWILL
08166643792
http://facebook.com/godswill.egegwu
http://egegwugodswill.name.ng
Challenges in deep learning methods for medical imaging - PubricaPubrica
1. Broad between association cooperation.
2. Need to Capitalize Big Image Data.
3. Progression in Deep Learning Methods.
4. Black-Box and Its Acceptance by Health Professional.
5. Security and moral issues.
6. Wrapping up.
Continue Reading: https://bit.ly/37zT2ur
Reference: https://pubrica.com/services/physician-writing-services/clinical-litearture-review-for-an-evidence-based-medicine/
Why Pubrica?
When you order our services, Plagiarism free|on Time|outstanding customer support|Unlimited Revisions support|High-quality Subject Matter Experts.
Contact us :
Web: https://pubrica.com/
Blog: https://pubrica.com/academy/
Email: sales@pubrica.com
WhatsApp : +91 9884350006
United Kingdom: +44- 74248 10299
The Amazing Ways Artificial Intelligence Is Transforming Genomics and Gene Ed...Bernard Marr
It is predicted that artificial intelligence (AI) will transform many aspects of our life including healthcare and genomics. AI and machine learning have helped us to understand the genome of organisms and will potentially change the way we treat disease, determine effective drugs and edit genes.
The adaptive mechanisms include the following AI paradigms that exhibit an ability to learn or adapt to new environments:
Swarm Intelligence (SI),
Artificial Neural Networks (ANN),
Evolutionary Computation (EC),
Artificial Immune Systems (AIS), and
Fuzzy Systems (FS).
This document summarizes research from the Finnish Center for Artificial Intelligence (FCAI).
1. FCAI conducts fundamental AI research and aims to apply this research to have high societal impact. It builds on decades of AI foundation work at universities in Finland.
2. FCAI's research focuses on understandable and data-efficient AI, including privacy-preserving machine learning and interactive expert knowledge elicitation to improve predictive models.
3. Other areas of research include modeling human-AI interaction, inverse modeling of user behavior, and endowing AI with a theory of mind to understand users.
This document is a 36-page bachelor's thesis written by Duc Minh Luong Nguyen titled "Detect COVID-19 from Chest X-Ray images using Deep Learning". The thesis was submitted to Metropolia University of Applied Sciences in May 2020. It aims to build a deep convolutional neural network to detect COVID-19 using only chest X-ray images. The model achieves an accuracy of 93% at detecting COVID-19 patients versus healthy patients, despite being trained on a small dataset of 115 images for each class.
Deep learning for biomedical discovery and data mining IIDeakin University
(1) The document discusses deep learning techniques for analyzing biomedical data from electronic medical records (EMRs).
(2) It describes models like DeepPatient that use autoencoders to learn representations of patient records that can predict diseases.
(3) Other models like Deepr and DeepCare use convolutional and recurrent neural networks to model temporal patterns in EMRs and predict future health risks and care trajectories.
Prospects of Deep Learning in Medical ImagingGodswll Egegwu
A SEMINAR Presentation on the Prospects of Deep Learning in Medical Imaging Presented to the Department of Computer Science, Nasarawa State Polytechnic, Lafia.
BY:
EGEGWU, GODSWILL
08166643792
http://facebook.com/godswill.egegwu
http://egegwugodswill.name.ng
Challenges in deep learning methods for medical imaging - PubricaPubrica
1. Broad between association cooperation.
2. Need to Capitalize Big Image Data.
3. Progression in Deep Learning Methods.
4. Black-Box and Its Acceptance by Health Professional.
5. Security and moral issues.
6. Wrapping up.
Continue Reading: https://bit.ly/37zT2ur
Reference: https://pubrica.com/services/physician-writing-services/clinical-litearture-review-for-an-evidence-based-medicine/
Why Pubrica?
When you order our services, Plagiarism free|on Time|outstanding customer support|Unlimited Revisions support|High-quality Subject Matter Experts.
Contact us :
Web: https://pubrica.com/
Blog: https://pubrica.com/academy/
Email: sales@pubrica.com
WhatsApp : +91 9884350006
United Kingdom: +44- 74248 10299
The Amazing Ways Artificial Intelligence Is Transforming Genomics and Gene Ed...Bernard Marr
It is predicted that artificial intelligence (AI) will transform many aspects of our life including healthcare and genomics. AI and machine learning have helped us to understand the genome of organisms and will potentially change the way we treat disease, determine effective drugs and edit genes.
The adaptive mechanisms include the following AI paradigms that exhibit an ability to learn or adapt to new environments:
Swarm Intelligence (SI),
Artificial Neural Networks (ANN),
Evolutionary Computation (EC),
Artificial Immune Systems (AIS), and
Fuzzy Systems (FS).
This document summarizes research from the Finnish Center for Artificial Intelligence (FCAI).
1. FCAI conducts fundamental AI research and aims to apply this research to have high societal impact. It builds on decades of AI foundation work at universities in Finland.
2. FCAI's research focuses on understandable and data-efficient AI, including privacy-preserving machine learning and interactive expert knowledge elicitation to improve predictive models.
3. Other areas of research include modeling human-AI interaction, inverse modeling of user behavior, and endowing AI with a theory of mind to understand users.
This document is a 36-page bachelor's thesis written by Duc Minh Luong Nguyen titled "Detect COVID-19 from Chest X-Ray images using Deep Learning". The thesis was submitted to Metropolia University of Applied Sciences in May 2020. It aims to build a deep convolutional neural network to detect COVID-19 using only chest X-ray images. The model achieves an accuracy of 93% at detecting COVID-19 patients versus healthy patients, despite being trained on a small dataset of 115 images for each class.
The document lists Shamik Tiwari's research publications and academic activities. It includes 5 published journal articles, 1 book chapter, and 2 accepted journal articles. It also lists that he coordinates academic monitoring, curriculum development, guides Ph.D. students, delivered lectures, and serves as a reviewer for several journals. He has also completed many online courses and achieved high student feedback for his online teaching.
IRJET- Classifying Chest Pathology Images using Deep Learning TechniquesIRJET Journal
This document discusses classifying chest pathology images using deep learning techniques. It explores using pre-trained convolutional neural networks (CNNs) to classify chest radiograph images as either healthy or pathological, and to identify specific pathologies. The document reviews previous work on applying deep learning to medical image analysis. It then proposes using features extracted from pre-trained CNN models to classify chest radiographs, focusing on classifying images as healthy vs. pathological as an important screening task. The strengths of deep learning approaches for analyzing various chest diseases are explored.
IRJET - Prediction of Autistic Spectrum Disorder based on Behavioural Fea...IRJET Journal
This document summarizes a research paper that aims to predict autism spectrum disorder (ASD) based on behavioral features using machine learning. The researchers collected ASD screening data from different age groups to develop and evaluate neural network models for predicting ASD. They achieved up to 90% accuracy in predicting ASD. The researchers concluded that machine learning is a promising approach for ASD prediction but noted limitations like lack of large datasets. They plan to improve the models by collecting more data from various sources.
Genome-wide transcription profiling is a powerful technique in studying disease susceptible footprints. Moreover, when applied to disease tissue it may reveal quantitative and qualitative alterations in gene expression that give information on the context or underlying basis for the disease and may provide a new diagnostic approach. However, the data obtained from high-density microarrays is highly complex and poses considerable challenges in data mining. Past researches prove that neuro diseases damage the brain network interaction, protein- protein interaction and gene-gene interaction. A number of neurological research paper also analyze the relationship among damaged part. Analysis of gene-gene interaction network drawn by using state-of-the-art gene database of Alzheimer’s patient can conclude a lot of information. In this paper we used gene dataset affected with Alzheimer’s disease and normal patient’s dataset from NCBI databank. After proper processing the .CEL affymetrix data using RMA, we use the processed data to find gene interaction outputs. Then we filter the output files using probe set filtering attributes p-value and fold count and draw a gene-gene interaction network. Then we analyze the interaction network using GeneMania software.
Motivational overview for why the medical image analysis need a volumetric equivalent of popular ImageNet database used in benchmarking deep learning architectures, and as a basis for transfer learning when not enough data is available for training the deep learning from scratch
New Research Articles 2019 October Issue Signal & Image Processing An Interna...sipij
Signal & Image Processing: An International Journal (SIPIJ)
ISSN: 0976 – 710X [Online]; 2229 - 3922 [Print]
http://www.airccse.org/journal/sipij/index.html
Current Issue; October 2019, Volume 10, Number 5
Free- Reference Image Quality Assessment Framework Using Metrics Fusion and Dimensionality Reduction
Besma Sadou1, Atidel Lahoulou2, Toufik Bouden1, Anderson R. Avila3, Tiago H. Falk3 and Zahid Akhtar4, 1Non Destructive Testing Laboratory, University of Jijel, Algeria, 2LAOTI laboratory, University of Jijel, Algeria, 3University of Québec, Canada and 4University of Memphis, USA
Test-cost-sensitive Convolutional Neural Networks with Expert Branches
Mahdi Naghibi1, Reza Anvari1, Ali Forghani1 and Behrouz Minaei2, 1Malek-Ashtar University of Technology, Iran and 2Iran University of Science and Technology, Iran
Robust Image Watermarking Method using Wavelet Transform
Omar Adwan, The University of Jordan, Jordan
Improvements of the Analysis of Human Activity Using Acceleration Record of Electrocardiographs
Itaru Kaneko1, Yutaka Yoshida2 and Emi Yuda3, 1&2Nagoya City University, Japan and 3Tohoku University, Japan
http://www.airccse.org/journal/sipij/vol10.html
deep learning applications in medical image analysis brain tumorVenkat Projects
The tremendous success of machine learning algorithms at image recognition tasks in recent years intersects with a time of dramatically increased use of electronic medical records and diagnostic imaging. This review introduces the machine learning algorithms as applied to medical image analysis, focusing on convolutional neural networks, and emphasizing clinical aspects of the _eld. The advantage of machine learning in an era of medical big data is that signi_cant hierarchal relationships within the data can be discovered algorithmically without laborious hand-crafting of features. We cover key research areas and applications of medical image classi_cation, localization, detection, segmentation, and registration. We conclude by discussing research obstacles, emerging trends, and possible future directions.
This document is a resume for Dr. Arulmurugan Ambikapathi that summarizes his expertise and achievements. It lists his educational background, including a Ph.D. and positions held at various academic and research institutions. It also outlines his research focus on image processing, analysis, and applications in computer vision, deep learning, and automated optical inspection. Major projects and awards are mentioned, demonstrating his leadership and accomplishments in industrial research and academic publications.
Machine learning algorithms show promise in improving medical image analysis and diagnosis by helping physicians more accurately interpret images. Such algorithms can be trained using labeled medical image data to learn the differences between benign and malignant tumors, and then apply that learning to analyze new images and predict the likelihood of tumors being benign or malignant. However, it is important to address the potential pitfalls of machine learning and ensure its safe and effective use in medical applications.
The Center for Applied Optimization at the University of Florida conducts interdisciplinary research in optimization involving faculty from various departments. Over the past 5 years, their research has included global optimization, optimization in biomedicine like predicting epileptic seizures, analyzing massive datasets like social networks, developing approximation algorithms, and algorithms for problems like multicast networks. Current projects also involve computational neuroscience, probabilistic classifiers in medicine, research on energy problems, and using Raman spectroscopy for cancer research. The Center collaborates with researchers from other institutions and hosts many visiting scholars each year.
The document discusses the potential applications of deep learning in healthcare. It begins by explaining that deep learning models can improve accuracy of diagnosis, prognosis, and risk prediction by analyzing large datasets. It then discusses how deep learning can optimize hospital processes like resource allocation and patient flow by early and accurate prediction of diseases. Finally, it mentions that deep learning can help identify patient subgroups for personalized and precision medicine approaches.
Talk entitled "from the Virtual Human to a Digital Me" presented at the Virtual Physiological Human 2012 Conference held at IET Savoy, Savoy Place, London, 18-20 September 2012.
This document summarizes Mansi Chowkkar's MSc research project on detecting breast cancer from histopathological images using deep learning and transfer learning. The research aims to classify images as malignant or benign with high accuracy and efficiency. It implements CNN and DenseNet-121 models, with the latter using transfer learning with pre-trained ImageNet weights. The research achieved 90.9% test accuracy with CNN and 88.03% accuracy with transfer learning. Related work discusses deep learning applications in healthcare, image processing techniques, prior research on DenseNet, and the use of transfer learning for medical image classification with limited data.
IRJET- Breast Cancer Prediction using Deep LearningIRJET Journal
This document discusses using deep learning to predict breast cancer based on tumor data. It proposes using a neural network model to classify tumors as malignant or benign. The key steps are:
1. Collecting and preprocessing tumor cell data to remove noise and inconsistencies.
2. Developing a neural network model and training it on labeled training data to learn patterns.
3. Testing the trained model on unlabeled testing data to evaluate its accuracy in classifying tumors.
The goal is to develop an accurate model to help doctors determine the critical condition of patients and classify difficult tumors.
This document discusses bioinformatics in the context of the Health Engineering degree at UMA. It begins by defining bioinformatics as an attractive new scientific field at the interface of computer science, biology, and mathematics for discovering new information about diseases and the human body. It then discusses what skills a bioinformatician may need, such as programming, biology knowledge, and statistics/mathematics. Finally, it notes that bioinformatics can be applied in engineering, computing, and clinical roles to facilitate difficult tasks, improve algorithms, and discover new biological insights with computers.
An Analysis of The Methods Employed for Breast Cancer Diagnosis IJORCS
This document analyzes various methods used for breast cancer diagnosis. It discusses that artificial neural networks (ANNs) have been widely applied and are shown to increase diagnostic accuracy compared to individual methods. Multiple neural networks together provide better results than single networks. Recent approaches combine ANNs with other techniques like fuzzy logic. Overall, ANNs have become a robust and accurate system for breast cancer diagnosis and extending their use could help other diseases.
This talk will cover various medical applications of deep learning including tumor segmentation in histology slides, MRI, CT, and X-Ray data. Also, more complicated tasks such as cell counting where the challenge is to count how many objects are in an image. It will also cover generative adversarial networks and how they can be used for medical applications. This presentation is accessible to non-doctors and non-computer scientists.
Beyond Broken Stick Modeling: R Tutorial for interpretable multivariate analysisPetteriTeikariPhD
This document provides information about Petteri Teikari, including his educational background and affiliation with the Singapore Eye Research Institute. It then lists several papers and resources related to broken stick modeling, nonlinear multivariate analysis, and variable importance measures in random forests. Specific topics covered include dynamic modeling of multivariate processes, joint frailty models, additive modeling, outcome weighted deep learning for combination therapies, survival trees, correlation and variable importance, and developing model-agnostic variable importance measures. Links are provided to papers, code implementations, and visualization resources.
Powering Biomedical Artificial Intelligence with a Holistic Knowledge Graph (...Catia Pesquita
Biomedical AI applications increasingly rely on multi-domain and heterogeneous data, especially in areas such as personalised medicine and systems biology. Biomedical Ontologies are a golden opportunity in this area because they add meaning to the underlying data which can be used to support heterogeneous data integration, provide scientific context to the data augmenting AI performance, and afford explanatory mechanisms allowing the contextualization of AI predictions. In particular, ontologies and knowledge graphs support the computation of semantic similarity between objects, providing an understanding of why certain objects are considered similar or different. This is a basic aspect of explainability and is at the core of many machine learning applications. However, when data covers multiple domains, it may be necessary to integrate different ontologies to cover the full semantic landscape of the underlying data.
In this talk I will present our recent work on building an integrated knowledge graph that is based on the semantic annotation and interlinking of heterogeneous data into a holistic semantic landscape that supports semantic similarity assessments. In this talk I will discuss the challenges in building the knowledge graph from public resources, the methodology we are using and the road-ahead in biomedical ontology and knowledge graph alignment as AI becomes an integral part of biomedical research.
This document presents the Concept Definition Generator (CDG), an open source tool for defining healthcare concepts using multilevel modeling specifications. The CDG allows domain experts to graphically represent healthcare concepts and automatically generate associated XML schemas. It was developed in Python with a wxPython graphical interface to run cross-platform. The CDG addresses the significant challenges of knowledge representation for semantic interoperability of electronic health records. Future work includes further standardizing healthcare terminologies and developing proper modeling tools.
The document lists Shamik Tiwari's research publications and academic activities. It includes 5 published journal articles, 1 book chapter, and 2 accepted journal articles. It also lists that he coordinates academic monitoring, curriculum development, guides Ph.D. students, delivered lectures, and serves as a reviewer for several journals. He has also completed many online courses and achieved high student feedback for his online teaching.
IRJET- Classifying Chest Pathology Images using Deep Learning TechniquesIRJET Journal
This document discusses classifying chest pathology images using deep learning techniques. It explores using pre-trained convolutional neural networks (CNNs) to classify chest radiograph images as either healthy or pathological, and to identify specific pathologies. The document reviews previous work on applying deep learning to medical image analysis. It then proposes using features extracted from pre-trained CNN models to classify chest radiographs, focusing on classifying images as healthy vs. pathological as an important screening task. The strengths of deep learning approaches for analyzing various chest diseases are explored.
IRJET - Prediction of Autistic Spectrum Disorder based on Behavioural Fea...IRJET Journal
This document summarizes a research paper that aims to predict autism spectrum disorder (ASD) based on behavioral features using machine learning. The researchers collected ASD screening data from different age groups to develop and evaluate neural network models for predicting ASD. They achieved up to 90% accuracy in predicting ASD. The researchers concluded that machine learning is a promising approach for ASD prediction but noted limitations like lack of large datasets. They plan to improve the models by collecting more data from various sources.
Genome-wide transcription profiling is a powerful technique in studying disease susceptible footprints. Moreover, when applied to disease tissue it may reveal quantitative and qualitative alterations in gene expression that give information on the context or underlying basis for the disease and may provide a new diagnostic approach. However, the data obtained from high-density microarrays is highly complex and poses considerable challenges in data mining. Past researches prove that neuro diseases damage the brain network interaction, protein- protein interaction and gene-gene interaction. A number of neurological research paper also analyze the relationship among damaged part. Analysis of gene-gene interaction network drawn by using state-of-the-art gene database of Alzheimer’s patient can conclude a lot of information. In this paper we used gene dataset affected with Alzheimer’s disease and normal patient’s dataset from NCBI databank. After proper processing the .CEL affymetrix data using RMA, we use the processed data to find gene interaction outputs. Then we filter the output files using probe set filtering attributes p-value and fold count and draw a gene-gene interaction network. Then we analyze the interaction network using GeneMania software.
Motivational overview for why the medical image analysis need a volumetric equivalent of popular ImageNet database used in benchmarking deep learning architectures, and as a basis for transfer learning when not enough data is available for training the deep learning from scratch
New Research Articles 2019 October Issue Signal & Image Processing An Interna...sipij
Signal & Image Processing: An International Journal (SIPIJ)
ISSN: 0976 – 710X [Online]; 2229 - 3922 [Print]
http://www.airccse.org/journal/sipij/index.html
Current Issue; October 2019, Volume 10, Number 5
Free- Reference Image Quality Assessment Framework Using Metrics Fusion and Dimensionality Reduction
Besma Sadou1, Atidel Lahoulou2, Toufik Bouden1, Anderson R. Avila3, Tiago H. Falk3 and Zahid Akhtar4, 1Non Destructive Testing Laboratory, University of Jijel, Algeria, 2LAOTI laboratory, University of Jijel, Algeria, 3University of Québec, Canada and 4University of Memphis, USA
Test-cost-sensitive Convolutional Neural Networks with Expert Branches
Mahdi Naghibi1, Reza Anvari1, Ali Forghani1 and Behrouz Minaei2, 1Malek-Ashtar University of Technology, Iran and 2Iran University of Science and Technology, Iran
Robust Image Watermarking Method using Wavelet Transform
Omar Adwan, The University of Jordan, Jordan
Improvements of the Analysis of Human Activity Using Acceleration Record of Electrocardiographs
Itaru Kaneko1, Yutaka Yoshida2 and Emi Yuda3, 1&2Nagoya City University, Japan and 3Tohoku University, Japan
http://www.airccse.org/journal/sipij/vol10.html
deep learning applications in medical image analysis brain tumorVenkat Projects
The tremendous success of machine learning algorithms at image recognition tasks in recent years intersects with a time of dramatically increased use of electronic medical records and diagnostic imaging. This review introduces the machine learning algorithms as applied to medical image analysis, focusing on convolutional neural networks, and emphasizing clinical aspects of the _eld. The advantage of machine learning in an era of medical big data is that signi_cant hierarchal relationships within the data can be discovered algorithmically without laborious hand-crafting of features. We cover key research areas and applications of medical image classi_cation, localization, detection, segmentation, and registration. We conclude by discussing research obstacles, emerging trends, and possible future directions.
This document is a resume for Dr. Arulmurugan Ambikapathi that summarizes his expertise and achievements. It lists his educational background, including a Ph.D. and positions held at various academic and research institutions. It also outlines his research focus on image processing, analysis, and applications in computer vision, deep learning, and automated optical inspection. Major projects and awards are mentioned, demonstrating his leadership and accomplishments in industrial research and academic publications.
Machine learning algorithms show promise in improving medical image analysis and diagnosis by helping physicians more accurately interpret images. Such algorithms can be trained using labeled medical image data to learn the differences between benign and malignant tumors, and then apply that learning to analyze new images and predict the likelihood of tumors being benign or malignant. However, it is important to address the potential pitfalls of machine learning and ensure its safe and effective use in medical applications.
The Center for Applied Optimization at the University of Florida conducts interdisciplinary research in optimization involving faculty from various departments. Over the past 5 years, their research has included global optimization, optimization in biomedicine like predicting epileptic seizures, analyzing massive datasets like social networks, developing approximation algorithms, and algorithms for problems like multicast networks. Current projects also involve computational neuroscience, probabilistic classifiers in medicine, research on energy problems, and using Raman spectroscopy for cancer research. The Center collaborates with researchers from other institutions and hosts many visiting scholars each year.
The document discusses the potential applications of deep learning in healthcare. It begins by explaining that deep learning models can improve accuracy of diagnosis, prognosis, and risk prediction by analyzing large datasets. It then discusses how deep learning can optimize hospital processes like resource allocation and patient flow by early and accurate prediction of diseases. Finally, it mentions that deep learning can help identify patient subgroups for personalized and precision medicine approaches.
Talk entitled "from the Virtual Human to a Digital Me" presented at the Virtual Physiological Human 2012 Conference held at IET Savoy, Savoy Place, London, 18-20 September 2012.
This document summarizes Mansi Chowkkar's MSc research project on detecting breast cancer from histopathological images using deep learning and transfer learning. The research aims to classify images as malignant or benign with high accuracy and efficiency. It implements CNN and DenseNet-121 models, with the latter using transfer learning with pre-trained ImageNet weights. The research achieved 90.9% test accuracy with CNN and 88.03% accuracy with transfer learning. Related work discusses deep learning applications in healthcare, image processing techniques, prior research on DenseNet, and the use of transfer learning for medical image classification with limited data.
IRJET- Breast Cancer Prediction using Deep LearningIRJET Journal
This document discusses using deep learning to predict breast cancer based on tumor data. It proposes using a neural network model to classify tumors as malignant or benign. The key steps are:
1. Collecting and preprocessing tumor cell data to remove noise and inconsistencies.
2. Developing a neural network model and training it on labeled training data to learn patterns.
3. Testing the trained model on unlabeled testing data to evaluate its accuracy in classifying tumors.
The goal is to develop an accurate model to help doctors determine the critical condition of patients and classify difficult tumors.
This document discusses bioinformatics in the context of the Health Engineering degree at UMA. It begins by defining bioinformatics as an attractive new scientific field at the interface of computer science, biology, and mathematics for discovering new information about diseases and the human body. It then discusses what skills a bioinformatician may need, such as programming, biology knowledge, and statistics/mathematics. Finally, it notes that bioinformatics can be applied in engineering, computing, and clinical roles to facilitate difficult tasks, improve algorithms, and discover new biological insights with computers.
An Analysis of The Methods Employed for Breast Cancer Diagnosis IJORCS
This document analyzes various methods used for breast cancer diagnosis. It discusses that artificial neural networks (ANNs) have been widely applied and are shown to increase diagnostic accuracy compared to individual methods. Multiple neural networks together provide better results than single networks. Recent approaches combine ANNs with other techniques like fuzzy logic. Overall, ANNs have become a robust and accurate system for breast cancer diagnosis and extending their use could help other diseases.
This talk will cover various medical applications of deep learning including tumor segmentation in histology slides, MRI, CT, and X-Ray data. Also, more complicated tasks such as cell counting where the challenge is to count how many objects are in an image. It will also cover generative adversarial networks and how they can be used for medical applications. This presentation is accessible to non-doctors and non-computer scientists.
Beyond Broken Stick Modeling: R Tutorial for interpretable multivariate analysisPetteriTeikariPhD
This document provides information about Petteri Teikari, including his educational background and affiliation with the Singapore Eye Research Institute. It then lists several papers and resources related to broken stick modeling, nonlinear multivariate analysis, and variable importance measures in random forests. Specific topics covered include dynamic modeling of multivariate processes, joint frailty models, additive modeling, outcome weighted deep learning for combination therapies, survival trees, correlation and variable importance, and developing model-agnostic variable importance measures. Links are provided to papers, code implementations, and visualization resources.
Powering Biomedical Artificial Intelligence with a Holistic Knowledge Graph (...Catia Pesquita
Biomedical AI applications increasingly rely on multi-domain and heterogeneous data, especially in areas such as personalised medicine and systems biology. Biomedical Ontologies are a golden opportunity in this area because they add meaning to the underlying data which can be used to support heterogeneous data integration, provide scientific context to the data augmenting AI performance, and afford explanatory mechanisms allowing the contextualization of AI predictions. In particular, ontologies and knowledge graphs support the computation of semantic similarity between objects, providing an understanding of why certain objects are considered similar or different. This is a basic aspect of explainability and is at the core of many machine learning applications. However, when data covers multiple domains, it may be necessary to integrate different ontologies to cover the full semantic landscape of the underlying data.
In this talk I will present our recent work on building an integrated knowledge graph that is based on the semantic annotation and interlinking of heterogeneous data into a holistic semantic landscape that supports semantic similarity assessments. In this talk I will discuss the challenges in building the knowledge graph from public resources, the methodology we are using and the road-ahead in biomedical ontology and knowledge graph alignment as AI becomes an integral part of biomedical research.
This document presents the Concept Definition Generator (CDG), an open source tool for defining healthcare concepts using multilevel modeling specifications. The CDG allows domain experts to graphically represent healthcare concepts and automatically generate associated XML schemas. It was developed in Python with a wxPython graphical interface to run cross-platform. The CDG addresses the significant challenges of knowledge representation for semantic interoperability of electronic health records. Future work includes further standardizing healthcare terminologies and developing proper modeling tools.
An Introduction to Bioinformatics
Drexel University INFO648-900-200915
A Presentation of Health Informatics Group 5
Cecilia Vernes
Joel Abueg
Kadodjomon Yeo
Sharon McDowell Hall
Terrence Hughes
Data supporting precision oncology fda wakibbeWarren Kibbe
This document discusses how data is supporting precision oncology through three main points:
1) Our ability to generate and analyze biomedical data continues to grow in terms of variety and volume from sources like genomics and imaging.
2) Analyzing multi-scale, multi-modal temporal data requires advances in data science like machine learning and artificial intelligence.
3) Standards like FAIR data principles are needed to enable data sharing and the creation of a learning health system for cancer through harmonization and interoperability of data.
Cancer is a dangerous ailment that influences any part of the body and could produce malignant tumors. One feature of cancer is that abnormal cells create quickly and expand beyond their regular bounds. This could attack various parts of the human body and spread to other organs, which is the primary cause of cancer death. Cancer is becoming a more serious worldwide health concern. In the face of these threats, advanced technologies such as Artificial Intelligence (AI), cognitive systems, and the Internet of Things (IoT) may be insufficient to prevent, predict, diagnose, and treat cancer. Digital Twins (DT) with a combination of IoT, AI, cloud computing, and communications technologies such as 5G and 6G have the potential to significant reduce serious cancer threats. Observing data from DT populations may aid in the improvement of some cancer screening, prediction, prevention, detection, treatment, and research investment strategies. Applications of DT medicine specifically cancer, have been studied and analyzed in this paper using both conceptual and statistical analyses. This paper also shows a tree of some ailments where DT is applicable in their study. To the best of our knowledge, there is no literature research on various illnesses and DT specifically cancer disorders. To show the potential of DT, development hurdles of utilizing DT in cancer diseases are discussed, and then, several open research directions will be explained.
Free webinar-introduction to bioinformatics - biologist-1Elia Brodsky
The Omics Logic Introduction to Bioinformatics program is a one-month online training program that provides an introduction to the field of bioinformatics for beginners. The program consists of six sessions taught by an international team of experts, covering topics like genomics, transcriptomics, statistical analysis, machine learning, and a final bioinformatics project. Participants will learn data analysis skills in Python and R and how to extract insights from multi-omics datasets with applications in biomedicine. The goal is to prepare students for data-driven research in life sciences through interactive lessons, coding exercises, and independent projects.
Framework for understanding data science.pdfMichael Brodie
The objective of my research is to provide a framework with which the data science community can understand, define, and develop data science as a field of inquiry. The framework is based on the classical reference framework (axiology, ontology, epistemology, methodology) used for 200 years to define knowledge discovery paradigms and disciplines in the humanities, sciences, algorithms, and now data science. I augmented it for automated problem-solving with (methods, technology, community) [1][2]. The resulting data science reference framework is used to define the data science knowledge discovery paradigm in terms of the philosophy of data science addressed in [1] and the data science problem-solving paradigm, i.e., the data science method, and the data science problem-solving workflow, addressed in [2][3]. The framework is a much called for unifying framework for data science as it contains the components required to define data science. For insights to better understand data science, this paper uses the framework to define the emerging, often enigmatic, data science problem-solving paradigm and workflow, and to compare them with their well-understood scientific counterparts – scientific problem-solving paradigm and workflow.
The objective of my current research [4] is to develop a 21st C re-conception of data. Unlike 20th C data that are assets, 21st C data science data is phenomenological – a resource in which to discover phenomena and their properties, previously and otherwise impossible.
[1] Brodie, M.L., Defining data science: a new field of inquiry, arXiv preprint https://doi.org/10.48550/arXiv.2306.16177 Harvard University, July 2023.
[2] Brodie, M.L., A data science axiology: the nature, value, and risks of data science, arXiv preprint http://arxiv.org/abs/2307.10460 Harvard University, July 2023.
[3] Brodie, M.L., A framework for understanding data science, arXiv preprint https://arxiv.org/abs/2403.00776 Harvard University, March 2024.
[4] Brodie, M.L., Re-conceiving data in the 21st Century. Work in progress, Harvard University.
[DSC Europe 23][DigiHealth] Anja Baresic 0- Croatian digital Healthcare ecosy...DataScienceConferenc1
The document summarizes Croatia's efforts to develop its digital healthcare ecosystem and the role of artificial intelligence. It discusses how AI is being applied in medicine to decrease administrative burdens, improve hospital management, get results faster, and increase diagnostic accuracy. It provides examples of AI models being used for tasks like medical transcription and arrhythmia detection. It also addresses issues like data quality and sharing, regulatory efforts like the EU's AI Act, and Croatia's AI4Health.Cro hub which aims to support AI innovation and provide services like skills training, networking and investment support.
Gilbertson J, Schubert E, Richert C, Aijazi M, Becich MJ. "Multimedia Tools Propel Web Based Telepathology." Telemedicine and Telehealth Networks, 2(10) 31-36, Nov 1996.
[DSC Europe 23][DigiHealth] Dimitrios Kalogeropoulos A Sustainable Future for...DataScienceConferenc1
Dr Dimitrios Kalogeropoulos discusses risks and challenges with open learning AI in healthcare from 2003 to 2023. Key points include:
1) AI may restrict, discriminate, or exclude patients from treatment.
2) Issues around privacy/security attacks, deep fakes, and data poisoning.
3) Threats to digital sovereignty and economies from misuse of AI.
4) Lack of high-quality clinical trials and real-world data hinders adoption of AI in healthcare.
I have framed this talk to encourage Pharmacy students to embrace computing in general, and data science and artificial intelligence techniques in particular. The reason is that data-driven science has overtaken traditional lab science; chemistry and biology that underlie pharmacy have become data-driven sciences, and a significant majority of the new jobs in pharma industries demand data analysis skills. Increasingly, traditional bioinformatics approaches are being complemented or replaced by machine learning or deep learning algorithms, especially for cases that have large data sets. I will provide a few examples (e.g., drug discovery, finding adverse drug reactions and broadly pharmacovigilance, and selecting patients for clinical trials) to demonstrate how big data and/or AI are indispensable to pharma research and industry today.
CINECA webinar slides: Open science through fair health data networks dream o...CINECAProject
Since the FAIR data principles were published in 2016, many organizations including science funders and governments have adopted these principles to promote and foster true open science collaborations. However, to define a vision and create a video of a Personal Health Train that leverages worldwide FAIR health data in a federated manner is one step. To actually make this happen at scale and be able to show new scientific and medical insights for it is quite another!
In this webinar, we will dive into the basics of FAIR health data, but also take stock of the current situation in health data networks: after a year of frantic research and collaborations and many open datasets and hackathons on COVID-19, has the situation actually improved? Are we sharing health data on a global scale to improve medical practice, or is quality medical data still only accessible to researchers with the right credentials and deep pockets?
This webinar is part of the “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing. CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions.
This webinar took place on 21st January 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Themes and objectives:
To position FAIR as a key enabler to automate and accelerate R&D process workflows
FAIR Implementation within the context of a use case
Grounded in precise outcomes (e.g. faster and bigger science / more reuse of data to enhance value / increased ability to share data for collaboration and partnership)
To make data actionable through FAIR interoperability
Speakers:
Mathew Woodwark,Head of Data Infrastructure and Tools, Data Science & AI, AstraZeneca
Erik Schultes, International Science Coordinator, GO-FAIR
Georges Heiter, Founder & CEO, Databiology
Medical Assistant Design during this Pandemic Like Covid-19AI Publications
In the current world scenario, individuals square measure additional involved regarding their health. However, it's terribly troublesome to get consultation with the doctor just in case of any health problems. Since the invention of the Coronavirus (nCOV-19), it's become a world pandemic. At an equivalent time, it's been a good challenge to hospitals or health care employees to manage the flow of the high variety of cases. particularly in remote areas, it's becoming tougher to consult a doctor once the immediate hit of the epidemic has occurred. So, to steer an honest life, care is incredibly vital. The planned plan is to form a medical chatbot victimization Machine Learning algorithm which will diagnose the illness and supply basic details regarding the illness before consulting a doctor. Several studies will solve this downside with some reasonably chatbot or health assistant. This project report proposes a colloquial care larva that's designed to order, counsel and provides data on generic medicines for diseases to the patients. During this paper, we would like to explore and deepen additional information regarding chatbots that would facilitate individuals to urge an equivalent and correct treatment as a doctor would do. In addition, presenting a virtual assistant may live with the infection severity and connect with registered doctors once symptoms become serious.
Is Pervasive Healthcare Old Wine on a New Bottle?Jakob Bardram
The document discusses the concept of pervasive healthcare and provides examples of pervasive healthcare technologies and research. It defines pervasive healthcare as applying ubiquitous computing technologies to healthcare to make it available everywhere and integrate it more seamlessly into daily life. Examples discussed include home health monitoring systems, interactive hospital displays to improve awareness and coordination, and a context-aware patient safety system in operating rooms.
Explainable AI in Healthcare: Enhancing Transparency and Trust upon Legal and...IRJET Journal
This document discusses explainable artificial intelligence (XAI) and its importance in healthcare. It explores how XAI can enhance transparency and trust in AI systems used for clinical decision-making. Various XAI techniques like rule-based models, decision trees and model-agnostic methods are described. The document also examines the legal and ethical considerations of applying XAI in healthcare and discusses challenges and future directions.
The document discusses explainable AI (XAI) methods. It defines XAI both narrowly as techniques that explain model decisions and broadly as anything that increases AI understandability. The document outlines intrinsically interpretable and post-hoc explanation methods like LIME and SHAP that explain complex models. It emphasizes the importance of explanations being actionable, contextualized and developed with stakeholder input. The document presents examples of XAI dashboards and concludes with recommendations to involve end-users and provide personalized, simplified explanations.
The document summarizes Anita de Waard's presentation on Elsevier's experiments with big and small data. It discusses Elsevier's work with text mining and knowledge graphs to extract information from over 14 million articles. It also describes Elsevier's Medical Graph which predicts the probability of over 2,000 medical conditions occurring based on analysis of clinical data from 6 million patients. Finally, it reviews Elsevier's various tools and services to help researchers preserve, process, share, comprehend, access, and discover research data and publications.
Similar a Knowledge Science for AI-based biomedical and clinical applications (20)
Open Source Contributions to Postgres: The Basics POSETTE 2024ElizabethGarrettChri
Postgres is the most advanced open-source database in the world and it's supported by a community, not a single company. So how does this work? How does code actually get into Postgres? I recently had a patch submitted and committed and I want to share what I learned in that process. I’ll give you an overview of Postgres versions and how the underlying project codebase functions. I’ll also show you the process for submitting a patch and getting that tested and committed.
Beyond the Basics of A/B Tests: Highly Innovative Experimentation Tactics You...Aggregage
This webinar will explore cutting-edge, less familiar but powerful experimentation methodologies which address well-known limitations of standard A/B Testing. Designed for data and product leaders, this session aims to inspire the embrace of innovative approaches and provide insights into the frontiers of experimentation!
Predictably Improve Your B2B Tech Company's Performance by Leveraging DataKiwi Creative
Harness the power of AI-backed reports, benchmarking and data analysis to predict trends and detect anomalies in your marketing efforts.
Peter Caputa, CEO at Databox, reveals how you can discover the strategies and tools to increase your growth rate (and margins!).
From metrics to track to data habits to pick up, enhance your reporting for powerful insights to improve your B2B tech company's marketing.
- - -
This is the webinar recording from the June 2024 HubSpot User Group (HUG) for B2B Technology USA.
Watch the video recording at https://youtu.be/5vjwGfPN9lw
Sign up for future HUG events at https://events.hubspot.com/b2b-technology-usa/
End-to-end pipeline agility - Berlin Buzzwords 2024Lars Albertsson
We describe how we achieve high change agility in data engineering by eliminating the fear of breaking downstream data pipelines through end-to-end pipeline testing, and by using schema metaprogramming to safely eliminate boilerplate involved in changes that affect whole pipelines.
A quick poll on agility in changing pipelines from end to end indicated a huge span in capabilities. For the question "How long time does it take for all downstream pipelines to be adapted to an upstream change," the median response was 6 months, but some respondents could do it in less than a day. When quantitative data engineering differences between the best and worst are measured, the span is often 100x-1000x, sometimes even more.
A long time ago, we suffered at Spotify from fear of changing pipelines due to not knowing what the impact might be downstream. We made plans for a technical solution to test pipelines end-to-end to mitigate that fear, but the effort failed for cultural reasons. We eventually solved this challenge, but in a different context. In this presentation we will describe how we test full pipelines effectively by manipulating workflow orchestration, which enables us to make changes in pipelines without fear of breaking downstream.
Making schema changes that affect many jobs also involves a lot of toil and boilerplate. Using schema-on-read mitigates some of it, but has drawbacks since it makes it more difficult to detect errors early. We will describe how we have rejected this tradeoff by applying schema metaprogramming, eliminating boilerplate but keeping the protection of static typing, thereby further improving agility to quickly modify data pipelines without fear.
Orchestrating the Future: Navigating Today's Data Workflow Challenges with Ai...Kaxil Naik
Navigating today's data landscape isn't just about managing workflows; it's about strategically propelling your business forward. Apache Airflow has stood out as the benchmark in this arena, driving data orchestration forward since its early days. As we dive into the complexities of our current data-rich environment, where the sheer volume of information and its timely, accurate processing are crucial for AI and ML applications, the role of Airflow has never been more critical.
In my journey as the Senior Engineering Director and a pivotal member of Apache Airflow's Project Management Committee (PMC), I've witnessed Airflow transform data handling, making agility and insight the norm in an ever-evolving digital space. At Astronomer, our collaboration with leading AI & ML teams worldwide has not only tested but also proven Airflow's mettle in delivering data reliably and efficiently—data that now powers not just insights but core business functions.
This session is a deep dive into the essence of Airflow's success. We'll trace its evolution from a budding project to the backbone of data orchestration it is today, constantly adapting to meet the next wave of data challenges, including those brought on by Generative AI. It's this forward-thinking adaptability that keeps Airflow at the forefront of innovation, ready for whatever comes next.
The ever-growing demands of AI and ML applications have ushered in an era where sophisticated data management isn't a luxury—it's a necessity. Airflow's innate flexibility and scalability are what makes it indispensable in managing the intricate workflows of today, especially those involving Large Language Models (LLMs).
This talk isn't just a rundown of Airflow's features; it's about harnessing these capabilities to turn your data workflows into a strategic asset. Together, we'll explore how Airflow remains at the cutting edge of data orchestration, ensuring your organization is not just keeping pace but setting the pace in a data-driven future.
Session in https://budapestdata.hu/2024/04/kaxil-naik-astronomer-io/ | https://dataml24.sessionize.com/session/667627
Knowledge Science for AI-based biomedical and clinical applications
1. Knowledge Science for AI-based
biomedical and clinical applications
Catia Pesquita
LASIGE, University of Lisbon
@CPesquita clpesquita@fc.ul.pt
TOWARDS TRUSTWORTHY DATA
First International Workshop on Knowledge Science
March 31, 2022
Eindhoven Artificial Intelligence Systems Institute
2. Why biomedical AI needs Knowledge
Science
1. Large amounts of data in
non-standard formats which
need to be converted, interpreted, and
merged into readable formats.
2. Heterogeneous and complex
data which current ML/AI
approaches are processing without
context
3. Lack of explainability
hinders trust
2
Knowledge Science is key to tackle ALL challenges
3. Trust in AI
• the user successfully comprehends how the model arrives
at an outcome 🡪 represent inputs, outputs and processes
• the model’s outcomes/workings match the user’s prior
knowledge 🡪 build a shared context
3
Jacovi, Alon, et al. "Formalizing trust in artificial intelligence: Prerequisites, causes and goals of human
trust in AI." Proceedings of the 2021 ACM conference on fairness, accountability, and transparency. 2021.
4. Trust in AI
• the user successfully comprehends how the model arrives
at an outcome 🡪 represent a model’s processes represent
inputs, outputs and
• the model’s outcomes/workings match the user’s prior
knowledge 🡪 evaluation
4
5. What happens when data
is complex, multi-domain,
heterogeneous,
incomplete, ambiguous?
5
6. Trust in AI for biomedical and clinical
applications
• the user successfully comprehends how the model arrives
at an outcome 🡪 represent a model’s processes represent
inputs, outputs and
• the model’s outcomes/workings match the user’s prior
knowledge 🡪 evaluation
6
7. Trust in AI for biomedical and clinical
applications
• the user successfully comprehends how the model arrives
at an outcome 🡪 represent a model’s inputs, outputs and
processes
• the model’s outcomes/workings match the user’s prior
knowledge 🡪 evaluation
7
8. Trust in AI for biomedical and clinical
applications
• the user successfully comprehends how the model arrives
at an outcome 🡪 represent a model’s inputs, outputs and
processes
• the model’s outcomes/workings match the user’s prior
knowledge 🡪 represent the scientific context
8
9. Knowledge Science can help mitigate
bias in biomedical AI
9
10.1038/s43856-021-00028-w
Mitigating bias in machine learning for medicine
10. Knowledge Science for Trust in
Biomedical AI
Assessing trustworthiness requires data, domain and user
context
Data context: represent data provenance and
transformations/processing
Domain/background knowledge: represent the scientific
context of the data and application
User context: different users will trust based on different
expectations
10
11. Data Context
Augment explanations with the data creation and processing
context
• Provide a rich contextual semantic layer to the underlying
data using domain ontologies and knowledge graphs.
• Preserve uncertainty and highlight potential ambiguity
and incompleteness at the data level
11
12. Data Context is key for trust
25% of the works that developed ML approaches to
diagnose COVID-19 in adults based on chest X-rays and CT
scans used pediatric
(ages 1-5) pneumonia
images as control.
12
Roberts, Michael, et al. "Common pitfalls and recommendations for using machine learning to detect and prognosticate for
COVID-19 using chest radiographs and CT scans." Nature Machine Intelligence 3.3 (2021): 199-217.
10.1016/j.cell.2018.02.0
10
COVID-19
10.1016/j.rxeng.2020.11.0
01
13. Domain Knowledge Context
Contextualize an explanation within existing knowledge
• Include prior knowledge through links to ontologies
• Enrich the contextual semantic layer with links and
relations across domains of knowledge
13
15. Domain Knowledge Context is key for
trust
15
Gingiva Gum
0.98
Term 1 Term 2 Similarity
Gingiva Gum 0.98
Anatomical
Part
Chemical
Substance
16. User Context
Trusting an AI outcome depends on the user context: task,
prior knowledge, expectation, etc.
16
Protein A and Protein B
are not similar at all since
they are involved in
unrelated diseases…
Protein A and Protein B
are very similar because
they perform the same
molecular function!
Biochemist Clinician
18. NextGen Biomedical AI requires
integration of complex and diverse data
Molecular
Cellular
Anatomy
Phenotype
and Disease
Clinical
18
Environmental
19. • 100s of very large files per patient covering genome
sequence, mutations, transcriptome, clinical, etc.
19
NextGen Biomedical AI requires
integration of complex and diverse data
20. What happens when data
is complex, multi-domain,
heterogeneous,
incomplete, ambiguous?
20
21. One ontology is not enough
Systems Biology,
Systems Medicine and
Personalized Medicine
require holistic
representations
21
JD Ferreira, DC Teixeira, C Pesquita. Biomedical Ontologies: Coverage, Access and Use. 2020 Systems Medicine Integrative, Qualitative and Computational
Approaches, Academic Press, Elsevier
22. What do we need to create holistic
representations?
Cover multiple
domains
Align multiple ontologies
Scalability
Ensure rich semantic
integration
Related but not equal
domains
Complex relations involving
more than one ontology
Provide high quality
alignments
Support human interaction
Visualizing the context of a
mapping
Balancing cognitive
overload and
informativeness
22
MC Silva, D Faria, and C Pesquita. Integrating knowledge graphs for explainable artificial intelligence in biomedicine. Ontology Matching workshop 2021
23. Rethinking biomedical ontology
alignment
Cover multiple
domains
Pairwise ontology
alignment
Holistic ontology
alignment of multiple
ontologies
Ensure rich semantic
integration
Simple equivalence
ontology alignment
Complex ontology
alignment
Provide high quality
alignments
User
validation
Human-in-the-loop
Interactive Alignment
23
MC Silva, D Faria, and C Pesquita. Integrating knowledge graphs for explainable artificial intelligence in biomedicine. Ontology Matching workshop 2021
24. Holistic Matching with clustering and incremental
matching
24
Silva, M.C., Faria, D. & Pesquita, C. (2022). Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine. ESWC2022 (accepted)
Can we ensure the scalability of matching tasks with many
ontologies?
25. Holistic Matching (CIA) runs in half the time, ensures
high recall within similar domains and high precision
across domains
25
Silva, M.C., Faria, D. & Pesquita, C. (2022). Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine.
ESWC2022 (accepted)
26. Compound Matching for ontology triples
Can we find mappings involving multiple ontologies using
lexical approaches and search space pruning?
26
HP:0001650
aortic stenosis
PATO:0001847
constricted
Step 1
FMA:3734
aorta
Step 2
HP:0001650
(…) stenosis
Filter unmapped source classes
Remove mapped words from class labels.
Selection of best scoring mappings
Oliveira, D., & Pesquita, C. (2018). Improving the interoperability of biomedical ontologies with compound alignments. J. Biomedical Semantics.
Ontology sets Correct (New)
MP-CL-PATO 47.1% (17.6%)
MP-GO-PATO 86.9% (22.3%)
MP-NBO-PATO 70.4% (20.7%)
MP-UBERON-PATO 83.5% (24.7%)
WBP-GO-PATO 44.9% (33.3%)
HP-FMA-PATO 81.5% (44.1%)
33. Patient
Ex-smoker
Smoker
Diabetes
MET
HLA-A2
cytokine-mediated
signaling pathway
Renal cell
carcinoma, somatic Sunitinib
Antineoplastic
Agent
Tyrosine kinase
activity
Cancer
AI recommendation
presents
has mutation
inhibits
The KG can be used to contextualize the
patient and the drug recommendation
promotes
treats
Patient
treated with
33
is risk factor
How diverse is
my dataset in
terms of patient
features?
35. Patient
Ex-smoker
Smoker
Diabetes
MET
HLA-A2
cytokine-mediated
signaling pathway
Renal cell
carcinoma, somatic Sunitinib
Antineoplastic
Agent
Tyrosine kinase
activity
Cancer
AI recommendation
presents
has mutation
inhibits
The KG can be used to contextualize the
patient and the drug recommendation
promotes
treats
Patient
treated with
35
is risk factor
How does the
prediction match
current scientific
knowledge?
36. Patient
Ex-smoker
Smoker
Diabetes
MET
HLA-A2
cytokine-mediated
signaling pathway
Renal cell
carcinoma, somatic Sunitinib
Antineoplastic
Agent
Tyrosine kinase
activity
Cancer
AI recommendation
presents
has mutation
inhibits
The KG can be used to contextualize the
patient and the drug recommendation
promotes
treats
Patient
treated with
36
is risk factor
How **similar** are
patients treated with
the same drug?
37. The great barrier to AI adoption in healthcare
and biomedical research is lack of trust.
Knowledge Science is the answer.
Photo by National Cancer Institute on Unsplash 37
38. Acknowledgements
Daniel Faria, LASIGE/Biodata.pt, Portugal
Isabel Cruz, U. Illinois, USA
Ernesto Jimenez-Ruiz, City, U. of London, UK
Daniela Oliveira, Novartis
Patrick Lambrix, U. Linkoping, Sweden
Valentina Ivanova, RISE, Sweden
Booma S. Balasubramani, Microsoft
and many others
Past and present students:
Rita Sousa
Marta Silva
Susana Nunes
Ana Guerreiro
Patrícia Eugénio
Filipa Serrano
Beatriz Lima
Carlota Cardoso
and many others
38
https://liseda-lab.github.io/
https://github.com/liseda-lab/
https://github.com/AgreementMakerLight
@CPesquita
clpesquita@fc.ul.pt
This work was supported by FCT through the
LASIGEResearch Unit (UIDB/00408/2020 and
UIDP/00408/2020). It was also partially supported by the
KATY project which has received funding from the European
Union’s Horizon 2020 research and innovation programme
under grant agreement No 101017453.