The 5th International Workshop
on Conceptual Modeling for Life Sciences

Logo CMLS

28th October, 2024 in Pittsburgh, Pennsylvania, US


In conjunction with the 43rd International Conference on Conceptual Modeling (ER 2024)

28th-31st October, 2024

Invited Talk

Ricardo Fernández-Ramires


Prof. Dr. Ricardo Fernández-Ramires is a distinguished genetic counselor specializing in clinical genetics and oncology. He obtained his PhD in Molecular Biology from the Spanish National Cancer Center (CNIO) in Madrid. He also completed a fellowship at the Catalan Oncology Institute (ICO) in Barcelona. Currently, Dr. Fernández-Ramires heads the Chilean Hereditary Cancer Group and holds academic positions as a professor at Universidad Mayor and Universidad de Chile.

Title:Facing Latin America genomic diversity: One size does not fit all

Talk abstract: Latin America is a region characterized by rich genetic diversity, shaped by a complex history of Indigenous, European, and African admixture. However, this diversity is significantly underrepresented in global genomic databases. Most existing genomic data comes from populations of European descent, leading to a biased understanding of human genetics and creating challenges for non-European populations, especially in Latin America. This underrepresentation has direct consequences for precision medicine and healthcare outcomes. Genomic studies and treatments that rely on these limited datasets may not be fully applicable or effective for Latin American populations, leading to disparities in diagnosis, treatment, and prevention strategies. In the context of hereditary cancer, the lack of representation in genomic databases complicates the diagnosis and management of high-risk patients in Latin America. Identifying pathogenic variants associated with hereditary cancer is more difficult when the variants are not well-documented or studied. Additionally, the prevalence of Variants of Uncertain Significance (VUS), which are common in Latin American populations, poses a significant challenge for clinicians. VUS are genetic changes with unknown biological impact, making it harder to provide clear guidance for patient care. These variants may be specific to the region, further complicating their interpretation. Addressing these issues requires more robust inclusion of Latin American populations in genomic research and expanding the catalog of pathogenic variants relevant to this region. This would not only improve the diagnosis and treatment of hereditary cancer but also enhance precision medicine efforts by tailoring healthcare to the unique genetic makeup of Latin American populations. Expanding representation in global genomic datasets is essential for closing the gap in healthcare disparities and advancing equitable healthcare across diverse populations.

About

The recent advances in unraveling the secrets of human conditions and diseases have encouraged new paradigms for their prevention, diagnosis, and treatment. As information is increasing at an unprecedented rate, it directly impacts the design and future development of information and data management pipelines; thus, new ways of processing data, information, and knowledge in healthcare environments are strongly needed.
The fifth edition of the workshop aims to continue being a meeting point for Information Systems (IS), Conceptual Modeling (CM), Data Management (DM), and Artificial Intelligence (AI) researchers working on health care and life science problems. It is also an opportunity to share, discuss and find new approaches to improve promising fields, with a special focus on Genomic Data Management – how to use the information from the genome to better understand biological and clinical features – and Precision Medicine – giving to each patient an individualized treatment by understanding the peculiar aspects of the disease.
From the precise ontological characterization of the components involved in complex biological systems to the modeling of the operational processes and decision support methods used in the diagnosis and prevention of diseases, the joined research communities of IS, CM, DM, and AI have an important role to play; they must help in providing feasible solutions for high-quality and efficient health care.
CMLS aims to become a forum for discussing the responsibility of the conceptual modeling community in supporting the life sciences related to these new realities.

Topics of interest

The fifth edition of the workshop focuses on Conceptual Modeling as a means for facing the challenges that emerge when designing and developing systems for life sciences, focused on genomics and precision medicine. The workshop is not restricted to specific research methods; we will consider both conceptual and empirical research, as well as novel applications.

The topics of interest include, but are not limited to:

  • AI and life science
  • Large Language Models for improving precision medicine and decision making
  • Conceptual models for data-driven AI systems in life sciences
  • Conceptual modeling for genomics
  • Modeling of complex biological systems and health ecosystems
  • Information systems for healthcare, genomics, or medicine of precision
  • Design, implementation, and evaluation of health information systems
  • Electronic/digital health information systems
  • Life science-related domain-specific modeling languages
  • Data management and integration for genomics and biology
  • Ontologies and workflows for life sciences
  • Clinical and biological data interoperability
  • Interoperability of health information systems
  • Knowledge representation for genetics
  • Business process modeling for genetic/clinical diagnosis
  • Conceptual model-driven big data analytics for genomics, clinical diagnosis, or biological problems
  • Models for the digital transformation of healthcare systems
  • Conceptual models in life sciences: from theory to practice
  • Models to facilitate multidisciplinary exchange in healthcare contexts
  • Virology-related conceptual models and their applications
  • Conceptual models and information systems for fighting climate change and its effects
  • Reviews focusing on a particular life science dimension

Accepted papers

The list of accepted papers for CMLS 2024:

  • Luis Henrique Costa Neto, Sérgio Lifschitz, Fernanda Baiao, Marcos Catanho, Antonio Basílio de Miranda and Edward Hermann Haeusler. On the Expressiveness of Petri Nets for Modeling Biological Processes the Case for mRNA Translation and Protein Synthesis
  • Yichao Chen, Yongqun He and Yuhan Zhang. Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features
  • Diana Martínez-Minguet and Óscar Pastor. Conceptual Modeling for Polygenic Risk Score Research: Improving Domain Understanding and Clinical Utility
  • Yujia Tian, Yongqun He, Rachel Richesson and Melvin Mclnnis. Integrative Ontology of Bipolar Disorder (OBD): Advancing Bipolar Disorder Research through an Interoperable Ontological Framework

Paper submission guidelines

We invite submissions of high quality papers describing original and unpublished results regarding any of the workshop’s topics of interest.

CMLS 2024 proceedings will be part of the ER 2024 Workshop volume published by Springer in the LNCS series. The authors must submit manuscripts using the Springer-Verlag LNCS style for Lecture Notes in Computer Science. For style files and details, see the page https://www.springer.com/gp/computer-science/lncs/conference-proceedings-guidelines. The page limit for workshop papers is 10 pages (plus 1-page references). Papers must be submitted as PDF files using EasyChair at https://easychair.org/my/conference?conf=er2024, choosing the track 'CMLS Workshop Paperes'.

To ensure high quality, all papers will be thoroughly peer reviewed by the Program Committee. Manuscripts not submitted in the LNCS style or having more than 10 pages will not be reviewed and thus automatically rejected. The papers need to be original and not submitted or accepted for publication in any other workshop, conference, or journal. Submission to CMLS 2024 will be electronically only. Papers will be judged on contribution, literature basis, novelty, clarity, relevance, and rigor. The review process is double-blind. Submissions must be anonymized.

Important dates

  • Abstract submission: July 13th, 2024 (OPTIONAL)
  • Paper submission: July 27th, 2024 August 4th, 2024 (EXTENDED)
  • Notification: August 11th, 2024 August 15th, 2024 (DELAYED)
  • Camera-ready version AND Author Registration: August 30th, 2024
  • ER conference dates: October 28th-31st, 2024

Organizers

albertogarcias
Alberto García S., Valencian Research Institute for Artificial Intelligence (VRAIN)
Universitat Politècnica de València, Spain
algarsi3@pros.upv.es

Alberto García S. obtained his Ph.D. cum laude at Universitat Politecnica de Valencia under the supervision of Prof. Oscar Pastor. He is currently a researcher at the VRAIN research institute, where he focuses on conceptual modeling, data science, and User Interface design. He has participated in multiple research projects in collaboration with clinicians and geneticists to generate knowledge from genomics data effectively and efficiently.



annabernasconi
Anna Bernasconi, Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB)
Politecnico di Milano, Italy
anna.bernasconi@polimi.it

Anna Bernasconi is Assistant Professor at the Department of Electronics, Information, and Bioengineering at Politecnico di Milano and has been Visiting Research Fellow at Universitat Politecnica de Valencia. Her research areas are Bioinformatics, Databases, and Data Science, where she applies conceptual modeling, data integration, and knowledge engineering in several life sciences and other applied sciences domains, with a focus on building open-source tools and services. Since the COVID-19 pandemic, her research has moved to viral genomics, by building models, databases, and Web search systems for viral sequences and their variants. She co-organized and chaired the first four International Workshops on Conceptual Modeling for Life Sciences (CMLS 2020 through 2023) and the first three International Workshops on Web Applications for Life Sciences (WALS 2022 through 2024) co-located with the ICWE conference.



josereyes
José Fabián Reyes Román, Valencian Research Institute for Artificial Intelligence (VRAIN)
Universitat Politècnica de València, Spain
jreyes@pros.upv.es

José F. Reyes R. is a Postdoctoral researcher and PMO at PROS Research Center at Universitat Politècnica de València (Spain). He holds a Ph.D. in Computer Sciences (2018) from Universitat Politècnica de València (UPV, Spain), a MSc in Software Engineering, Formal Methods and Information Systems (2013) from UPV (Spain), a Diplomate of Analysts and Systems Designers (2011) and a University Degree in System Engineering (2010) from Universidad Central del Este (Dominican Republic). Currently, his main research interests include Conceptual Modeling, Genomic Data Science, Explainable AI, Engineering Requirements, SE, and Information Systems Engineering. From a conceptual modeling perspective, he develops solutions in the genomic and clinical domain.

Edelweis Rohrer
Edelweis Rohrer,
Facultad de Ingeniería of Universidad de la República, Uruguay
erohrer@fing.edu.uy

Edelweis Rohrer is a researcher and associte professor. She also serves as the head of the Software Engineering Department at the General Accounting of the Ministry of Economy of Uruguay. She holds a Ph.D. in design and foundations of ontologies with metamodelling, and a Master of Science degree in methodologies on ontology engineering, both from Universidad de la República, Uruguay. Her current lines of interest are ontological engineering and reasoning applied to the health field, particularly in detecting and preventing breast cancer.



Program Committee (in progress)

  • Bernardo Breve, Università degli Studi di Salerno, Italy
  • Raffaele Calogero, University of Turin
  • Stefano Ceri, Politecnico di Milano
  • Stefano Cirillo, Università degli Studi di Salerno, Italy
  • Nelly Condori, Universidad Santiago de Compostela, Spain
  • Tommaso Dolci, Politecnico di Milano
  • Giovanni Giachetti, Universitat Politècnica de València, Spain
  • Giancarlo Guizzardi, University of Twente, Netherlands
  • Sergio Lifschitz, Pontifical Catholic University of Rio de Janeiro, Brazil
  • Giovanni Meroni, Technical University of Denmark
  • Paolo Missier, Newcastle University, United Kingdom
  • José Palazzo, Federal University of Rio Grande do Sul, Brazil
  • Ignacio Panach, University of Valencia, Spain
  • Oscar Pastor, Universitat Politècnica de València
  • Barbara Pernici, Polytechnic University of Milan, Italy
  • Tiago Prince Sales, University of Twente, The Netherlands
  • Monjoy Saha, National Cancer Institute, USA
  • Veda Storey, Georgia State University, USA
  • Lisa Trigiante, University of Modena and Reggio Emilia, Italy
  • Juan Carlos Trujillo, University of Alicante, Spain

Program

The workshop will run on Monday October 28th, 2024.
Please refer to the ER conference website for information on the full conference program (ER 2024 program).


09.00-09.10
Welcome and introduction to the CMLS workshop

09.10-10.20
Invited Talk by Prof. Dr. Ricardo Fernández-Ramires, Universidad Mayor, Chile Facing Latin America genomic diversity: One size does not fit al

10.20-10.40
Yichao Chen, Yongqun He and Yuhan Zhang Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features

10.40-11.00
Diana Martínez-Minguet and Óscar Pastor Conceptual Modeling for Polygenic Risk Score Research: Improving Domain Understanding and Clinical Utility

Coffee Break 11.00-11.30

11.30-11.50
Luis Henrique Costa Neto, Sérgio Lifschitz, Fernanda Baiao, Marcos Catanho, Antonio Basílio de Miranda and Edward Hermann Haeusler On the Expressiveness of Petri Nets for Modeling Biological Processes the Case for mRNA Translation and Protein Synthesis

11.50-12.10
Yujia Tian, Yongqun He, Rachel Richesson and Melvin Mclnnis Integrative Ontology of Bipolar Disorder (OBD): Advancing Bipolar Disorder Research through an Interoperable Ontological Framework

12.10-12.20
Closing

Collaborations

This workshop is supported by the data-driven Genomic Computing group at Politecnico di Milano and by the VRAIN Research Center at Universitat Politecnica de Valencia (grants: PID2021-123824OB-I00 and CIPROM/2021/023)

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